Repository 'cardinal_data_exporter'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter

Changeset 2:e30d8b72415f (2019-02-15)
Previous changeset 1:65ef413a35f3 (2018-10-25) Next changeset 3:d94770c22f13 (2019-02-28)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
modified:
data_exporter.xml
macros.xml
test-data/112_auto_combined_QC.pdf
test-data/123_combined.RData
test-data/123_combined_QC.pdf
test-data/12_combined.RData
test-data/12_combined_QC.pdf
test-data/2123_auto_combined.RData
test-data/2123_auto_combined_QC.pdf
test-data/Plot_empty_spectra.pdf
test-data/QC_analyze75.pdf
test-data/QC_empty_spectra.pdf
test-data/QC_imzml.pdf
test-data/QC_rdata.pdf
test-data/analyze75_filtered2.pdf
test-data/centroids_rdata.pdf
test-data/cluster_skm.RData
test-data/features_test2.tabular
test-data/features_test4.tabular
test-data/features_test6.tabular
test-data/features_test7.tabular
test-data/imzml_filtered3.pdf
test-data/imzml_filtered4.pdf
test-data/imzml_filtered5.pdf
test-data/kmeans_analyze.pdf
test-data/pca_imzml.pdf
test-data/pixel_out2.tabular
test-data/pixel_out3.tabular
test-data/preprocessing_results1.pdf
test-data/preprocessing_results2.pdf
test-data/preprocessing_results3.pdf
test-data/preprocessing_results4.pdf
test-data/preprocessing_results5.RData
test-data/preprocessing_results5.pdf
test-data/rdata_notfiltered.pdf
test-data/scores_pca.tabular
test-data/test1.pdf
test-data/test2.pdf
test-data/test2.rdata
test-data/test3.pdf
test-data/test4.pdf
test-data/test4.rdata
test-data/test5.pdf
test-data/test6.pdf
test-data/test6.rdata
test-data/test7.pdf
test-data/test7.rdata
added:
test-data/112_auto_combined.ibd
test-data/112_auto_combined.imzml
test-data/112_auto_combined.imzml.txt
test-data/123_annotation.ibd
test-data/123_annotation.imzml
test-data/123_auto_combined.imzml.txt
test-data/123_combined_auto.ibd
test-data/123_combined_auto.imzml
test-data/123_combined_auto.imzml.txt
test-data/123_combined_auto.pdf
test-data/123_combined_auto.tabular
test-data/out3.ibd
test-data/out3.imzml
test-data/out3.imzml.txt
test-data/out4.ibd
test-data/out4.imzml
test-data/out4.imzml.txt
test-data/out5.ibd
test-data/out5.imzml
test-data/out5.imzml.txt
test-data/out6.ibd
test-data/out6.imzml
test-data/out6.imzml.txt
test-data/out7.ibd
test-data/out7.imzml
test-data/out7.imzml.txt
test-data/preprocessing_results1.ibd
test-data/preprocessing_results1.imzml
test-data/preprocessing_results1.imzml.txt
test-data/preprocessing_results2.ibd
test-data/preprocessing_results2.imzml
test-data/preprocessing_results2.imzml.txt
test-data/preprocessing_results3.ibd
test-data/preprocessing_results3.imzml
test-data/preprocessing_results3.imzml.txt
test-data/preprocessing_results4.ibd
test-data/preprocessing_results4.imzml
test-data/preprocessing_results4.imzml.txt
removed:
test-data/112_auto_combined.RData
test-data/analyze_filtered.RData
test-data/analyze_filtered.pdf
test-data/analyze_filteredoutside.RData
test-data/analyze_originaloutput.RData
test-data/analyze_originaloutput2.RData
test-data/imzml_filtered.RData
test-data/imzml_filtered.pdf
test-data/imzml_filtered3.RData
test-data/imzml_filtered4.RData
test-data/imzml_filtered5.RData
test-data/loadings_pca.tabular
test-data/preprocessed.rdata
test-data/preprocessing_results1.RData
test-data/preprocessing_results1.txt
test-data/preprocessing_results2.RData
test-data/preprocessing_results2.txt
test-data/preprocessing_results3.RData
test-data/preprocessing_results4.RData
test-data/preprocessing_results4.txt
test-data/preprocessing_results5.txt
test-data/rdata_notfiltered.RData
b
diff -r 65ef413a35f3 -r e30d8b72415f data_exporter.xml
--- a/data_exporter.xml Thu Oct 25 07:26:29 2018 -0400
+++ b/data_exporter.xml Fri Feb 15 10:17:43 2019 -0500
[
b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.0">\n+<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.1">\n     <description>\n         exports imzML and Analyze7.5 to tabular files\n     </description>\n@@ -22,26 +22,28 @@\n \n library(Cardinal)\n \n-@READING_MSIDATA@\n+@READING_MSIDATA_INRAM@\n \n-npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)\n-\n-if (npeaks > 0){\n+## to make sure that processed files work as well: \n+iData(msidata) = iData(msidata)[]\n \n     ###################### Intensity matrix output ################################\n \n     #if "int_matrix" in str($output_options).split(","):\n         print("intensity matrix output")\n \n-        spectramatrix = spectra(msidata)[]\n         mz_names = gsub(" = ", "_", names(features(msidata)))\n         mz_names = gsub("/", "", mz_names)\n         pixel_names = gsub(", y = ", "_", names(pixels(msidata)))\n         pixel_names = gsub(" = ", "y_", pixel_names)\n \n-        spectramatrix = cbind(mz_names,spectramatrix)\n+        spectramatrix = cbind(mz_names,spectra(msidata)[])\n         newmatrix = rbind(c("mz_name", pixel_names), spectramatrix)\n         write.table(newmatrix, file="$intensity_matrix", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\\t")\n+        ## free up RAM space in case furhter steps will be run: \n+        rm(newmatrix)\n+        rm(spectramatrix)\n+        gc()\n \n     #end if\n \n@@ -59,6 +61,7 @@\n         full_sample_sd = apply(spectra(msidata)[],1,sd, na.rm=TRUE)\n         full_sample_sem = full_sample_sd/full_sample_mean*100\n         ## npeaks and sum of all intensities per spectrum and mz\n+        npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)\n         mzTIC = rowSums(spectra(msidata)[], na.rm=TRUE) ## calculate intensity sum for each m/z\n         peakspermz = rowSums(spectra(msidata)[] > 0, na.rm=TRUE) ## calculate number of intensities > 0 for each m/z (max = number of spectra)\n \n@@ -147,25 +150,30 @@\n         xycoordinates = coord(msidata)[,1:2]\n \n         ## pixel name\n-        pixel_names = gsub(", y = ", "_", names(pixels(msidata)))\n-        pixel_names = gsub(" = ", "y_", pixel_names)\n+        pixel_names = paste0("xy_", xycoordinates\\$x, "_", xycoordinates\\$y)\n \n         ## pixel order \n         pixelxyarray=1:length(pixels(msidata))\n \n         ## number of pixels per spectrum: every intensity value > 0 counts as peak\n-        peaksperpixel = colSums(spectra(msidata)[]> 0, na.rm=TRUE)\n+        peaksperpixel = apply(spectra(msidata)[]> 0, 2, sum, na.rm=TRUE)\n \n         ## Total ion chromatogram per spectrum\n-        TICs = round(colSums(spectra(msidata)[], na.rm=TRUE), digits = 2)\n+        TICs = round(apply(spectra(msidata)[],2, sum, na.rm=TRUE), digits = 2)\n+\n+        ## Median ion intensity per spectrum\n+        med_int = round(apply(spectra(msidata)[], 2, median, na.rm=TRUE), digits = 2)\n+\n+        ## Maximum ion intensity per spectrum\n+        max_int = round(apply(spectra(msidata)[], 2, max, na.rm=TRUE), digits = 2)\n \n         ## Highest m/z per spectrum\n         highestmz = apply(spectra(msidata)[],2,which.max) \n         highestmz_data = mz(msidata)[highestmz]\n \n         ## Combine into dataframe; order is the same for all vectors\n-        spectra_df = data.frame(pixel_names, xycoordinates, pixelxyarray, peaksperpixel, TICs, highestmz_data)\n-        colnames(spectra_df) = c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "spectrum_TIC", "most_abundant_mz")\n+        spectra_df = data.frame(pixel_names, xycoordinates, pixelxyarray, peaksperpixel, med_int, TICs, max_int, highestmz_data)\n+        colnames(spectra_df) = c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz")\n \n         #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":\n \n@@ -191,7 +199,8 @@\n                     filtered_data = msidata[mz(msidata) >= inputcalibrantmas'..b'ant m/z range with intensity > 0 is TRUE)\n-                countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE))\n+                countvector= as.factor(apply(pixelmatrix, 2,sum,na.rm=TRUE))\n+\n             }else{countvector = rep(0,ncol(msidata))}\n                 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts\n-                colnames(countdf) = c("x_values", "y_values", "input m/z count")\n+                colnames(countdf) = c("x_values", "y_values", "m/z count")\n                 spectra_df = merge(spectra_df, countdf, by=c("x_values", "y_values"))\n \n                 ## sort columns to have spectra_names as rowname in first column\n-                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "spectrum_TIC", "most_abundant_mz", "input m/z count")]\n+                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "m/z count")]\n \n         #end if\n         #if str($tabular_annotation.load_annotation) == \'yes_annotation\':\n@@ -218,9 +228,9 @@\n \n             ## sort columns to have spectra_names as rowname in first column\n             #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":\n-                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "spectrum_TIC", "most_abundant_mz", "input m/z count", "annotation")]\n+                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "m/z count", "annotation")]\n             #else\n-                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "spectrum_TIC", "most_abundant_mz", "annotation")]\n+                spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "annotation")]\n             #end if\n \n         #end if\n@@ -232,11 +242,6 @@\n     #end if\n \n \n-}else{\n-    print("file has no features or pixels left")\n-}\n-\n-\n     ]]></configfile>\n     </configfiles>\n     <inputs>\n@@ -247,7 +252,7 @@\n             <option value="pixel_tabular">pixel output</option>\n         </param>\n         <conditional name="counting_calibrants">\n-            <param name="pixel_with_calibrants" type="select" label="Add number of m/z of interest per spectrum to pixel output">\n+            <param name="pixel_with_calibrants" type="select" label="Use file with m/z of interest to calculate their occurrence in each spectrum">\n                 <option value="no_calibrants" selected="True">no</option>\n                 <option value="yes_calibrants">yes</option>\n             </param>\n@@ -349,7 +354,7 @@\n **Output options**\n \n - intensity matrix: m/z in rows, spectra in columns, filled with intensity values\n-- spectra output: spectra in rows - for each spectrum: name, x and y coordinates,order, number of peaks (intensities > 0), total ion chromatogram (TIC), highest m/z feature per spectrum, optional count of input m/z per spectrum, optional spectrum annotation\n+- spectra output: spectra in rows - for each spectrum: name, x and y coordinates,order, number of peaks (intensities > 0), total ion chromatogram (TIC), median intensity, maximum intensity, highest m/z feature per spectrum, optional count of m/z per spectrum, optional spectrum annotation\n - mz feature output: m/z in rows - for each m/z: name, m/z, mean, median, standard deviation (sd), standard error of the mean (sem), sum of all intensities per m/z, number of peaks (intensity > 0) per m/z\n - summarized intensities: pixel annotations will be used to group spectra into annotation groups and calculate mean, median and sd of the intensities per group\n \n'
b
diff -r 65ef413a35f3 -r e30d8b72415f macros.xml
--- a/macros.xml Thu Oct 25 07:26:29 2018 -0400
+++ b/macros.xml Fri Feb 15 10:17:43 2019 -0500
[
@@ -69,25 +69,92 @@
         ## Range y coordinates
         minimumy = min(coord(msidata)[,2])
         maximumy = max(coord(msidata)[,2])
+
+
+        properties = c("Number of m/z features",
+                       "Range of m/z values",
+                       "Number of pixels", 
+                       "Range of x coordinates", 
+                       "Range of y coordinates")
+
+        values = c(paste0(maxfeatures), 
+                   paste0(minmz, " - ", maxmz), 
+                   paste0(pixelcount), 
+                   paste0(minimumx, " - ", maximumx),
+                   paste0(minimumy, " - ", maximumy))
+
+        property_df = data.frame(properties, values)
+    ]]></token>
+
+    <token name="@READING_MSIDATA_INRAM@"><![CDATA[
+        ## importing MSI data files
+
+        ## function to read RData files independent of filename
+        loadRData <- function(fileName){
+        load(fileName)
+        get(ls()[ls() != "fileName"])
+        }
+
+        #if $infile.ext == 'imzml'
+            #if str($processed_cond.processed_file) == "processed":
+                msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
+                centroided(msidata) = $centroids
+            #else
+                msidata <- readImzML('infile')
+                centroided(msidata) = $centroids
+            #end if
+        #elif $infile.ext == 'analyze75'
+            msidata = readAnalyze('infile')
+            centroided(msidata) = $centroids
+        #else
+            msidata = loadRData('infile.RData')
+        #end if
+
+    ]]></token>
+
+    <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
+########################### QC numbers ########################
+## including intensity calculations which need data in RAM
+        ## Number of features (mz)
+        maxfeatures = length(features(msidata))
+        ## Range mz
+        minmz = round(min(mz(msidata)), digits=2)
+        maxmz = round(max(mz(msidata)), digits=2)
+        ## Number of spectra (pixels)
+        pixelcount = length(pixels(msidata))
+        ## Range x coordinates
+        minimumx = min(coord(msidata)[,1])
+        maximumx = max(coord(msidata)[,1])
+        ## Range y coordinates
+        minimumy = min(coord(msidata)[,2])
+        maximumy = max(coord(msidata)[,2])
         ## Range of intensities
         minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
         maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
         ## Number of intensities > 0, for if conditions
         npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
+        ## Number of NA in spectra matrix
+        NAcount = sum(is.na(spectra(msidata)[]))
+        ## Number of NA in spectra matrix
+        infcount = sum(is.infinite(spectra(msidata)[]))
 
         properties = c("Number of m/z features",
                        "Range of m/z values",
                        "Number of pixels", 
                        "Range of x coordinates", 
                        "Range of y coordinates",
-                       "Range of intensities")
+                       "Range of intensities", 
+                       "Number of NA intensities",
+                       "Number of Inf intensities")
 
         values = c(paste0(maxfeatures), 
                    paste0(minmz, " - ", maxmz), 
                    paste0(pixelcount), 
                    paste0(minimumx, " - ", maximumx),  
                    paste0(minimumy, " - ", maximumy), 
-                   paste0(minint, " - ", maxint))
+                   paste0(minint, " - ", maxint), 
+                   paste0(NAcount), 
+                   paste0(infcount))
 
         property_df = data.frame(properties, values)
     ]]></token>
@@ -144,9 +211,9 @@
     <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[
         - Optional file with pixel coordinates and annotation: 
 
-            - Tabular file: One column with x values, one column wiht y values and one column with annotations
+            - Tabular file: One column with x values, one column with y values and one column with annotations
             - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)
-            - Pixel with coordinates outside the coordinates of the input file are ignored 
+            - Pixel with coordinates outside the coordinates of the input file are ignored
 
                 ::
 
@@ -161,9 +228,9 @@
 
     <xml name="reading_msidata">
         <param name="infile" type="data" format="imzml,rdata,analyze75"
-               label="Input file as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
-                help="Upload composite datatype imzML (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
-        <param name="centroids" type="boolean" label="Is the input data centroided (picked)" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
+               label="MSI data"
+                help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload)"/>
+        <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/>
         <conditional name="processed_cond">
             <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file">
                 <option value="no_processed" selected="True">no</option>
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/112_auto_combined.RData
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/112_auto_combined.ibd
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/112_auto_combined.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/112_auto_combined.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,475 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{00A83E55-A8F8-41D4-BBAC-345FA77AAB7E}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9B17E43E3D3B35BE3CD0AE65F40E0C6B27C2752F" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="15" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spec'..b'cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=14" defaultArrayLength="0" index="14">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="15" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=15" defaultArrayLength="0" index="15">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="15" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/112_auto_combined.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/112_auto_combined.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 556
+-rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd
+-rw-r--r-- 1 meli meli  25466 Feb 12 12:25 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/112_auto_combined_QC.pdf
b
Binary file test-data/112_auto_combined_QC.pdf has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_annotation.ibd
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Binary file test-data/123_annotation.ibd has changed
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_annotation.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_annotation.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,394 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{6CA61EE8-F100-401D-ABEA-0F34970DF802}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="DA249749B3777448F38B3FF06498B6144E1526EF" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="9" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spect'..b'\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=11" defaultArrayLength="0" index="11">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="369572" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=12" defaultArrayLength="0" index="12">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="403168" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_auto_combined.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_auto_combined.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 556
+-rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd
+-rw-r--r-- 1 meli meli  25466 Feb 12 12:25 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_combined.RData
b
Binary file test-data/123_combined.RData has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_combined_QC.pdf
b
Binary file test-data/123_combined_QC.pdf has changed
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_combined_auto.ibd
b
Binary file test-data/123_combined_auto.ibd has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_combined_auto.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,394 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{7DC9B0BB-277B-4A92-8780-2879E0E6A8F2}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="6768CFB740661C3F0C560438B85A906EA05933D5" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="8" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="11" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spec'..b'cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="9" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=11" defaultArrayLength="0" index="11">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="10" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="369572" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=12" defaultArrayLength="0" index="12">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="11" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="403168" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_combined_auto.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.imzml.txt Fri Feb 15 10:17:43 2019 -0500
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@@ -0,0 +1,4 @@
+imzML file:
+total 452
+-rw-r--r-- 1 meli meli 436764 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli  21166 Feb 12 00:51 imzml
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_combined_auto.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/123_combined_auto.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined_auto.tabular Fri Feb 15 10:17:43 2019 -0500
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@@ -0,0 +1,13 @@
+x y sample_name
+1 1 msidata_1.RData
+1 2 msidata_1.RData
+1 3 msidata_1.RData
+7 1 msidata_2.RData
+8 1 msidata_2.RData
+7 2 msidata_2.RData
+8 2 msidata_2.RData
+7 3 msidata_2.RData
+8 3 msidata_2.RData
+1 9 msidata_3.RData
+1 10 msidata_3.RData
+1 11 msidata_3.RData
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/12_combined.RData
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/2123_auto_combined.RData
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/Plot_empty_spectra.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/QC_analyze75.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/QC_imzml.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/analyze75_filtered2.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/analyze_filtered.RData
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/analyze_filtered.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/centroids_rdata.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/features_test2.tabular
--- a/test-data/features_test2.tabular Thu Oct 25 07:26:29 2018 -0400
+++ b/test-data/features_test2.tabular Fri Feb 15 10:17:43 2019 -0500
b
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b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/features_test4.tabular
--- a/test-data/features_test4.tabular Thu Oct 25 07:26:29 2018 -0400
+++ b/test-data/features_test4.tabular Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -1,101 +1,101 @@\n mz\tncomp\tcolumn\tcoefficients\tloadings\tweights\n-912.877136230469\t3\tB\t0.00402511569666969\t-0.246308032464734\t-0.0998747661753797\n-928.8232421875\t3\tA\t0.00355204006388532\t0.273286934815558\t0.288081987978036\n-928.859680175781\t3\tB\t0.00304099166534859\t-0.180023925015396\t-0.0975882865489913\n-929.806274414062\t3\tA\t0.00301867966492034\t0.20461792386307\t0.204104875190971\n-928.786865234375\t3\tA\t0.00294246516676733\t0.279365597419633\t0.24012019090174\n-912.913208007812\t3\tB\t0.00221421341476842\t-0.25734495461644\t-0.123924205177262\n-906.357543945312\t3\tB\t0.0017751956946221\t0.0660711931225974\t-0.167734534471784\n-913.887756347656\t3\tB\t0.00169164545723661\t-0.0797847981582402\t-0.0542158398194389\n-907.400573730469\t3\tA\t0.00168976824209188\t-0.0553409573032757\t-0.0310185392575794\n-900.3271484375\t3\tA\t0.0016850771109767\t0.0635456830152988\t0.0623351620915374\n-928.896057128906\t3\tB\t0.00168450000766379\t-0.182486440635111\t-0.0950023449824687\n-922.355712890625\t3\tA\t0.00167096941795371\t0.0529977859368994\t0.0679949938623556\n-900.398864746094\t3\tA\t0.00166100096018687\t0.0406827592981194\t-0.010027514312194\n-960.315368652344\t3\tA\t0.00164686513200881\t0.0692239228029656\t0.0559857485267436\n-964.353698730469\t3\tA\t0.0016007991522707\t0.0487859885763137\t0.049315043939497\n-906.3935546875\t3\tA\t0.00157421991835154\t-0.184824638462265\t-0.161519730620847\n-964.316589355469\t3\tA\t0.00143180642589214\t0.0309764043652652\t0.0453653991628429\n-962.31494140625\t3\tA\t0.00141328760599612\t0.0642563963154312\t0.0454439922528048\n-929.879089355469\t3\tB\t0.00137108902531006\t-0.147152863346693\t-0.0787919913569194\n-900.434692382812\t3\tB\t0.00131488882358473\t-0.20214180256976\t-0.173026933354479\n-901.402526855469\t3\tA\t0.00131071912036092\t0.0193425453272541\t0.00416556425120399\n-922.391967773438\t3\tA\t0.00128195781418033\t0.0250080230991378\t0.0401690309084914\n-915.33251953125\t3\tA\t0.00127720082168308\t0.0472700250545067\t0.0476142683041524\n-938.310852050781\t3\tA\t0.00126979651175339\t0.0258332330864995\t0.0395551945184375\n-913.923889160156\t3\tB\t0.00125913909333928\t-0.116366449217641\t-0.0823808975691949\n-907.508483886719\t3\tA\t0.00123463128203684\t0.0286834379044553\t0.0416260189187914\n-974.356140136719\t3\tA\t0.00122974867070485\t0.0426004370460666\t0.0327898050985416\n-933.451599121094\t3\tA\t0.00122075781571264\t0.0189293266454833\t0.0363946273679358\n-910.352966308594\t3\tA\t0.00121465945239948\t0.0212318588989688\t0.0191774558940735\n-990.339538574219\t3\tA\t0.00120033930835288\t0.0471035220902788\t0.0441020126132822\n-984.41015625\t3\tA\t0.00117709585424916\t0.0256612782877473\t0.0364785894847815\n-922.319458007812\t3\tA\t0.00116343926435404\t0.0350575504771194\t0.049003566656031\n-945.825500488281\t3\tA\t0.00116281366134625\t0.0358386234196617\t0.039941557361758\n-914.429443359375\t3\tA\t0.00114751581370748\t0.0214325420152595\t0.0322577162355903\n-934.364013671875\t3\tA\t0.00111966105461266\t0.0261184955739278\t0.0277902861913678\n-945.788757324219\t3\tA\t0.0011140971316516\t0.0602657244502292\t0.0678490003014779\n-930.27978515625\t3\tA\t0.00111107830564362\t0.0548573050563774\t0.0541864639681832\n-987.41015625\t3\tA\t0.00109109627880292\t0.0259022291567729\t0.0348827329301489\n-917.320922851562\t3\tB\t0.00108811988692458\t-0.0380939775497376\t-0.0859734761406655\n-961.388977050781\t3\tA\t0.00108270610537361\t0.0208991144261707\t0.0235951714502884\n-949.244445800781\t3\tA\t0.00108094226185502\t0.0553461544724562\t0.0473287208302763\n-914.393310546875\t3\tA\t0.00107937289161071\t0.0186407876697643\t0.0213451871968151\n-923.37158203125\t3\tA\t0.00107406087109902\t0.0174157121297602\t0.0300927241546599\n-967.322998046875\t3\tA\t0.00106160501633174\t0.0413827618597132\t0.0291509896006055\n-961.314880371094\t3\tA\t0.00105652394646208\t0.0429555520663857\t0.0345573512639803\n-994.252197265625\t3\tA\t0.00105259315733988\t0.0465400676246555\t0.0444177569572566\n-945.348083496094\t3\tA\t0.00104820825219221\t0.00490478080758506\t0.00553720261210505\n-913.346313476562\t3\tA\t0.00103460925930171\t0.0189564108870971\t0.026732642281156\n-914.321105957031\t3\tA\t0.00103017762730726\t0.0282931942786005\t0.0284256699648362\n-929.442138671875\t3\tA\t0.0010240497'..b'\t3\tA\t0.001413\t0.064256\t0.045444\n+929.879089355469\t3\tB\t0.001371\t-0.147153\t-0.078792\n+900.434692382812\t3\tB\t0.001315\t-0.202142\t-0.173027\n+901.402526855469\t3\tA\t0.001311\t0.019343\t0.004166\n+922.391967773438\t3\tA\t0.001282\t0.025008\t0.040169\n+915.33251953125\t3\tA\t0.001277\t0.04727\t0.047614\n+938.310852050781\t3\tA\t0.00127\t0.025833\t0.039555\n+913.923889160156\t3\tB\t0.001259\t-0.116366\t-0.082381\n+907.508483886719\t3\tA\t0.001235\t0.028683\t0.041626\n+974.356140136719\t3\tA\t0.00123\t0.0426\t0.03279\n+933.451599121094\t3\tA\t0.001221\t0.018929\t0.036395\n+910.352966308594\t3\tA\t0.001215\t0.021232\t0.019177\n+990.339538574219\t3\tA\t0.0012\t0.047104\t0.044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b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/features_test6.tabular
--- a/test-data/features_test6.tabular Thu Oct 25 07:26:29 2018 -0400
+++ b/test-data/features_test6.tabular Fri Feb 15 10:17:43 2019 -0500
b
@@ -1,21 +1,21 @@
 mz r k s classes centers tstatistics p.values adj.p.values
-928.859680175781 2 3 2 B 43.9516959905118 0.541814677313986 0.607464263577403 1
-912.877136230469 2 3 2 B 55.419364071664 0.437808238568372 0.676846169835776 1
-913.887756347656 2 3 2 B 24.9140214890445 0.393340199810185 0.70766449744142 1
-930.862670898438 2 3 2 B 9.28583084091344 0.29858210475084 0.775329712997245 1
-913.923889160156 2 3 2 B 12.1491837287613 0.0960056413112618 0.926642424678888 1
-900.004699707031 2 3 2 A 2.29166666666667 0 1 1
+928.859680175781 2 3 2 B 43.951696 0.541815 0.607464 1
+912.877136230469 2 3 2 B 55.419364 0.437808 0.676846 1
+913.887756347656 2 3 2 B 24.914021 0.39334 0.707664 1
+930.862670898438 2 3 2 B 9.285831 0.298582 0.77533 1
+913.923889160156 2 3 2 B 12.149184 0.096006 0.926642 1
+900.004699707031 2 3 2 A 2.291667 0 1 1
 900.04052734375 2 3 2 A 3.125 0 1 1
-900.076354980469 2 3 2 A 3.33333333333333 0 1 1
-900.112182617188 2 3 2 A 3.45833333333333 0 1 1
-900.148010253906 2 3 2 A 3.29166666666667 0 1 1
+900.076354980469 2 3 2 A 3.333333 0 1 1
+900.112182617188 2 3 2 A 3.458333 0 1 1
+900.148010253906 2 3 2 A 3.291667 0 1 1
 900.183837890625 2 3 2 A 3.375 0 1 1
-900.219665527344 2 3 2 A 3.66666666666667 0 1 1
-900.255493164062 2 3 2 A 3.91666666666667 0 1 1
-900.291320800781 2 3 2 A 4.08333333333333 0 1 1
-900.3271484375 2 3 2 A 5.79166666666667 0 1 1
-900.362976074219 2 3 2 A 11.5416666666667 0 1 1
-900.398864746094 2 3 2 A 26.2083333333333 0 1 1
-900.434692382812 2 3 2 A 30.0416666666667 0 1 1
-900.470520019531 2 3 2 A 19.1666666666667 0 1 1
+900.219665527344 2 3 2 A 3.666667 0 1 1
+900.255493164062 2 3 2 A 3.916667 0 1 1
+900.291320800781 2 3 2 A 4.083333 0 1 1
+900.3271484375 2 3 2 A 5.791667 0 1 1
+900.362976074219 2 3 2 A 11.541667 0 1 1
+900.398864746094 2 3 2 A 26.208333 0 1 1
+900.434692382812 2 3 2 A 30.041667 0 1 1
+900.470520019531 2 3 2 A 19.166667 0 1 1
 900.50634765625 2 3 2 A 8.5 0 1 1
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/features_test7.tabular
--- a/test-data/features_test7.tabular Thu Oct 25 07:26:29 2018 -0400
+++ b/test-data/features_test7.tabular Fri Feb 15 10:17:43 2019 -0500
b
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/loadings_pca.tabular
--- a/test-data/loadings_pca.tabular Thu Oct 25 07:26:29 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,1200 +0,0 @@\n-mz\tPC1\tPC2\n-300.08\t-0.00431122859758329\t0.00526403166713949\n-300.17\t-0.000423445750267208\t0.00051702937765159\n-300.25\t4.65194150536899e-11\t-4.22150087099464e-11\n-300.33\t1.35108612188122e-11\t-1.22607072500498e-11\n-300.42\t1.05327734584566e-12\t-9.55817595104931e-13\n-300.5\t-8.10333136001904e-07\t9.89420809472527e-07\n-300.58\t-5.81387112967612e-07\t7.09876570972713e-07\n-300.67\t-1.07032789780076e-07\t1.3068757132126e-07\n-300.75\t3.41674858316537e-15\t-3.099477097213e-15\n-300.83\t1.91005306978273e-15\t-1.73400711936836e-15\n-300.92\t3.0935599995382e-16\t-2.77380998949046e-16\n-301\t-6.65648097524728e-19\t1.46948889144108e-18\n-301.08\t-6.24592367703673e-11\t7.62630392533733e-11\n-301.17\t-1.86468400473725e-11\t2.27678809866643e-11\n-301.25\t-1.54395235623673e-12\t1.88517524320557e-12\n-301.33\t2.98688326385702e-19\t-3.5847546239491e-19\n-301.42\t8.89316552145388e-20\t-1.13353541808862e-19\n-301.5\t-1.80421834428211e-18\t3.57218991846548e-18\n-301.58\t-4.42908079426941e-15\t5.40912624674897e-15\n-301.67\t-2.60749760943137e-15\t3.18475128356288e-15\n-301.75\t-4.40359280065527e-16\t5.39122160392572e-16\n-301.83\t-1.38008713975051e-18\t2.88001159253086e-18\n-301.92\t-1.40307577498072e-19\t2.77975673360276e-19\n-302\t3.62667249262872e-18\t-7.13083020490704e-18\n-302.08\t-1.08392092461489e-18\t2.3266850449903e-18\n-302.17\t-1.89685413709983e-19\t1.23861281753609e-19\n-302.25\t1.84071706842555e-19\t-4.72845441155538e-19\n-302.33\t2.65842917715123e-18\t-5.67839989734713e-18\n-302.42\t8.89384394284211e-19\t-1.78363962868074e-18\n-302.5\t-7.90254051855962e-19\t1.67197231393762e-18\n-302.58\t-2.54806306921044e-18\t4.84666648270261e-18\n-302.67\t0.00238735543431953\t0.00059717760153527\n-302.75\t0.0422753281275894\t0.0105748304975569\n-302.83\t0.0478251463644703\t0.0119630725230272\n-302.92\t0.0117873138328592\t0.00294850096557018\n-303\t0.000543891887813245\t0.000136050145022238\n-303.08\t7.47436204207542e-19\t-1.56423855319991e-18\n-303.17\t1.14392477830951e-19\t-2.37594932440985e-19\n-303.25\t-2.00896832566757e-18\t3.98635625264106e-18\n-303.33\t4.18546560129704e-06\t1.04696027795764e-06\n-303.42\t1.7855922607419e-06\t4.46651423688008e-07\n-303.5\t2.40845866549495e-07\t6.02456403664431e-08\n-303.58\t-1.26795648107974e-18\t2.62533136732221e-18\n-303.67\t-1.06780307773474e-18\t2.0810699955122e-18\n-303.75\t1.2643870416402e-18\t-2.51396059682868e-18\n-303.83\t0.00179950042171087\t-0.057307260525996\n-303.92\t0.00323910627580984\t-0.117042680086361\n-304\t-0.00221983247055412\t-0.135440075021637\n-304.08\t0.00167857919888097\t-0.0398049258709\n-304.17\t0.015254290192657\t0.012790595615181\n-304.25\t0.00615007956388472\t0.00664260824343149\n-304.33\t0.000463810193289094\t0.000732422023079692\n-304.42\t-0.0121864568041163\t-0.000404596261869822\n-304.5\t-0.0206720168643015\t-0.000503758798744126\n-304.58\t-0.0328176999234842\t-0.0126423547079233\n-304.67\t-0.0482606832428354\t-0.0105800636691633\n-304.75\t-0.0142742734952315\t-0.00471930409453522\n-304.83\t-0.00118635057916411\t-0.000662474245569403\n-304.92\t-0.00138871717853178\t-4.61060822079781e-05\n-305\t-0.0527117640926545\t-0.00175005607056224\n-305.08\t-0.0428954493028061\t-0.00142414962759593\n-305.17\t-0.00848209306364131\t-0.000281745808963649\n-305.25\t-1.99382379701303e-06\t-5.72938648410526e-07\n-305.33\t-3.36192825452903e-07\t-1.33981156083197e-07\n-305.42\t2.5761506940952e-12\t2.78245755255616e-12\n-305.5\t-3.48349631092745e-19\t7.59816858773693e-19\n-305.58\t-4.42256844036834e-06\t-1.4683141192802e-07\n-305.67\t-0.00571542047365585\t0.00879722931697928\n-305.75\t-0.0254911789946344\t0.0392460448983895\n-305.83\t-0.0105718033678137\t-0.00291019853705438\n-305.92\t0.00618064757489481\t-0.131084648437099\n-306\t-0.000838690930111978\t-0.0744131926836283\n-306.08\t-0.0130494766825355\t0.00166045771715343\n-306.17\t0.0331859098477607\t0.0161552601031249\n-306.25\t0.0699660376819185\t0.0184786284566642\n-306.33\t0.0225906387134967\t0.00565340171628555\n-306.42\t0.00212956077044587\t0.000533291798037169\n-306.5\t0.00298787533493201\t0.000738712875826988\n-306.58\t0.0950317607456352\t0.0237696453640889\n-306.67\t0.12310606507388\t0.0260031521356849\n-306.75\t0.0306645997652937\t-0.0571'..b'23546721038e-12\n-393.25\t-2.34036390405774e-11\t4.93900212123262e-13\n-393.33\t-3.56838704124608e-06\t4.07205506770384e-06\n-393.42\t-1.76198360856187e-06\t2.01068275372772e-06\n-393.5\t-0.00233992195400915\t0.00360244123900651\n-393.58\t-0.0224309026287285\t0.0345346530641351\n-393.67\t-0.0144781756530043\t0.0222906220696274\n-393.75\t-0.0026549293256643\t0.00408753337701366\n-393.83\t-3.04582339785289e-11\t3.47569898364536e-11\n-393.92\t-2.07692010278724e-10\t2.37007166468918e-10\n-394\t0.000989421728722559\t-0.0315093316645265\n-394.08\t0.00166917857982581\t-0.0531570081597263\n-394.17\t0.000515223006487019\t-0.0164551396233416\n-394.25\t4.55292483933701e-05\t-0.00146398008581852\n-394.33\t-3.80471565270782e-08\t5.85774621944284e-08\n-394.42\t-1.80262500024233e-14\t2.05689490369655e-14\n-394.5\t-7.7909656610118e-15\t8.88828831877814e-15\n-394.58\t1.12421356224445e-07\t-3.58019391594558e-06\n-394.67\t7.11020518802956e-08\t-2.26769779930263e-06\n-394.75\t0.000316047453349314\t-0.0100649148736834\n-394.83\t0.00229889763821647\t-0.073211172468377\n-394.92\t0.00150372971795886\t-0.0478880892309078\n-395\t0.000292705972843111\t-0.00932157526617029\n-395.08\t-0.00875103820451387\t0.00998622320294566\n-395.17\t-0.0126456283855077\t0.0144305240873075\n-395.25\t-0.00378465244012699\t0.00431884573343672\n-395.33\t-0.000315001652628076\t0.000359463270406603\n-395.42\t1.56478579106423e-07\t-4.9832493669199e-06\n-395.5\t4.95699913407887e-08\t-1.57861625005459e-06\n-395.58\t4.59965931477345e-09\t-1.46481706778349e-07\n-395.67\t-8.93363646461732e-07\t1.01945947057533e-06\n-395.75\t-5.28499859979223e-07\t6.03096163123705e-07\n-395.83\t0.0101721470821755\t0.00254460417531899\n-395.92\t0.0901124169298955\t0.0225408899978156\n-396\t0.0619057408174025\t0.0154852188209358\n-396.08\t0.0120686207083509\t0.00301886756043136\n-396.17\t2.13427762585755e-18\t-4.57591641293874e-18\n-396.25\t-5.93693477596822e-11\t6.77491676579856e-11\n-396.33\t-1.62663136152525e-11\t1.85622572248383e-11\n-396.42\t-1.09391652965735e-12\t1.24832003417318e-12\n-396.5\t6.43609376126285e-06\t1.60993663686421e-06\n-396.58\t2.04220500508587e-06\t5.10841013808235e-07\n-396.67\t1.90042568568878e-07\t4.75376068364845e-08\n-396.75\t-4.67251518868319e-15\t5.33097853187915e-15\n-396.83\t-2.35613979840554e-15\t2.69012387669633e-15\n-396.92\t-3.61561868840093e-16\t4.1275441396577e-16\n-397\t0.00683320944088087\t0.00170927192743568\n-397.08\t0.0508156173515183\t0.0127111145890864\n-397.17\t0.0315399671799999\t0.00788946701538054\n-397.25\t0.00571098525966419\t0.00142855664922875\n-397.33\t4.89969485396192e-19\t-1.19060334525639e-18\n-397.42\t2.22834919338454e-18\t-4.34732897976762e-18\n-397.5\t8.31147483196322e-19\t-1.78218120586324e-18\n-397.58\t7.14897520004991e-19\t-1.54051878724343e-18\n-397.67\t3.41887735034728e-06\t8.55204443656831e-07\n-397.75\t1.0035305688935e-06\t2.51025033637385e-07\n-397.83\t8.01158365214818e-08\t2.00403268096558e-08\n-397.92\t-1.9142113485302e-18\t3.69209812345875e-18\n-398\t-2.33556706483865e-18\t4.5182654397614e-18\n-398.08\t-0.00206607196679601\t0.00235769234822122\n-398.17\t-0.0225874349565933\t0.0257755896848458\n-398.25\t-0.0160218359330536\t0.0182832742502864\n-398.33\t-0.0026940895995632\t0.00307435297682499\n-398.42\t-3.76104775049341e-18\t8.41246115765971e-18\n-398.5\t2.39548120740311e-20\t-5.08280982949083e-20\n-398.58\t5.66389784439603e-19\t-1.12520168973942e-18\n-398.67\t0.00295354336564466\t0.0016465989339032\n-398.75\t0.100753555082997\t0.0424027103707126\n-398.83\t0.0858729519853825\t0.0359862357359944\n-398.92\t0.0173733382364934\t0.00713147150476632\n-399\t4.58678491672166e-19\t-1.05711764259232e-18\n-399.08\t-3.74124159573477e-18\t8.10123796770424e-18\n-399.17\t1.44107919235719e-18\t-2.94492407411307e-18\n-399.25\t-2.28306806332197e-18\t4.56015944945022e-18\n-399.33\t8.7259811334237e-06\t3.70432674670869e-06\n-399.42\t2.88619885891337e-06\t1.19693828706317e-06\n-399.5\t2.87745593745991e-07\t1.14900342939911e-07\n-399.58\t3.43909756603207e-18\t-7.1235425369153e-18\n-399.67\t5.41775952563231e-19\t-1.17632377804067e-18\n-399.75\t-2.94880449307325e-20\t5.68563417987762e-20\n-399.83\t5.28798133253926e-10\t2.33513647021011e-10\n-399.92\t3.87854520523766e-10\t1.62263513454245e-10\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out3.ibd
b
Binary file test-data/out3.ibd has changed
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out3.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out3.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,151 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{AEDF2DEE-A321-4DAF-B971-943AE2AF79A6}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="8311A159EC925605745E409F14BB6C570FF59ACA" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spect'..b'x" value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2416" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=2" defaultArrayLength="0" index="2">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4816" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=3" defaultArrayLength="0" index="3">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="7216" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="600" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2400" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out3.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out3.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 24
+-rw-r--r-- 1 meli meli 9616 Feb 12 19:18 ibd
+-rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out4.ibd
b
Binary file test-data/out4.ibd has changed
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out4.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out4.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,205 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{2567A8C4-D2AF-4C81-874C-82E9134A080C}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="EA722C9CF5A229ACF6AEAD177908D73A1C8CB44E" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spect'..b'"1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="14404" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=4" defaultArrayLength="0" index="4">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="19200" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=5" defaultArrayLength="0" index="5">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="23996" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1199" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4796" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out4.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out4.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 44
+-rw-r--r-- 1 meli meli 28792 Feb 12 00:49 ibd
+-rw-r--r-- 1 meli meli 11141 Feb 12 00:49 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out5.ibd
b
Binary file test-data/out5.ibd has changed
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out5.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out5.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,232 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{CC0B2B92-FB40-42C8-822F-834AA528954C}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0B644915E88274BE83FBB110D4CC6D0CDFABAAAC" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spect'..b'0050" name="position x" value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="224" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=5" defaultArrayLength="0" index="5">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="276" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=6" defaultArrayLength="0" index="6">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="328" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="52" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out5.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out5.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 20
+-rw-r--r-- 1 meli meli   380 Feb 12 00:50 ibd
+-rw-r--r-- 1 meli meli 12508 Feb 12 00:50 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out6.ibd
b
Binary file test-data/out6.ibd has changed
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out6.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,313 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{24BF18EC-E1DE-4B67-BC12-C3EB475CFC0A}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="DA0417F6AA4EDD71F808B6EA0D7A0706737464EB" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spect'..b'\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3672" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="14688" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="102832" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3672" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="14688" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3672" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="14688" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="117520" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3672" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="14688" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3672" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="14688" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="132208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3672" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="14688" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out6.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out6.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 164
+-rw-r--r-- 1 meli meli 146896 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli  16868 Feb 12 00:51 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out7.ibd
b
Binary file test-data/out7.ibd has changed
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out7.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,313 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{B095BB77-684D-4BFF-82D3-B76D0EB1C0CD}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="628A551B81DCF301B65E3A5AB1182F0BF319533C" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spect'..b'"1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67188" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="76784" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="86380" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="9596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/out7.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out7.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 116
+-rw-r--r-- 1 meli meli 95976 Feb 12 00:51 ibd
+-rw-r--r-- 1 meli meli 16846 Feb 12 00:51 imzml
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/pca_imzml.pdf
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Binary file test-data/pca_imzml.pdf has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/pixel_out2.tabular
--- a/test-data/pixel_out2.tabular Thu Oct 25 07:26:29 2018 -0400
+++ b/test-data/pixel_out2.tabular Fri Feb 15 10:17:43 2019 -0500
b
@@ -1,10 +1,10 @@
-spectra_names x_values y_values pixel_order peaks_per_spectrum spectrum_TIC most_abundant_mz annotation
-xy_1_1 1 1 1 3672 42479 1267.525390625 col1
-xy_2_1 2 1 2 3672 29179 1264.42407226562 col2
-xy_3_1 3 1 3 3672 37005 1267.525390625 col3
-xy_1_2 1 2 4 3672 42306 1264.38171386719 col1
-xy_2_2 2 2 5 3672 30350 1267.525390625 col2
-xy_3_2 3 2 6 3672 35955 1199.55615234375 col3
-xy_1_3 1 3 7 3672 43872 1199.59753417969 col1
-xy_2_3 2 3 8 3672 33204 1267.48278808594 col2
-xy_3_3 3 3 9 3672 37961 1199.55615234375 col3
+spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz annotation
+xy_1_1 1 1 1 3672 11 42479 43 1267.525390625 col1
+xy_2_1 2 1 2 3672 8 29179 20 1264.42407226562 col2
+xy_3_1 3 1 3 3672 9 37005 42 1267.525390625 col3
+xy_1_2 1 2 4 3672 11 42306 49 1264.38171386719 col1
+xy_2_2 2 2 5 3672 8 30350 21 1267.525390625 col2
+xy_3_2 3 2 6 3672 9 35955 39 1199.55615234375 col3
+xy_1_3 1 3 7 3672 11 43872 84 1199.59753417969 col1
+xy_2_3 2 3 8 3672 9 33204 26 1267.48278808594 col2
+xy_3_3 3 3 9 3672 10 37961 47 1199.55615234375 col3
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/pixel_out3.tabular
--- a/test-data/pixel_out3.tabular Thu Oct 25 07:26:29 2018 -0400
+++ b/test-data/pixel_out3.tabular Fri Feb 15 10:17:43 2019 -0500
b
@@ -1,10 +1,10 @@
-spectra_names x_values y_values pixel_order peaks_per_spectrum spectrum_TIC most_abundant_mz input m/z count
-xy_1_1 1 1 1 241 22.92 329.083343505859 0
-xy_2_1 2 1 2 332 29.26 328.916687011719 0
-xy_3_1 3 1 3 415 24.43 328.916687011719 0
-xy_1_2 1 2 4 343 39.62 329 0
-xy_2_2 2 2 5 301 18.34 328.916687011719 0
-xy_3_2 3 2 6 194 10.79 345.083343505859 0
-xy_1_3 1 3 7 308 14.68 328.916687011719 0
-xy_2_3 2 3 8 367 24.87 329 0
-xy_3_3 3 3 9 323 35.18 329.083343505859 0
+spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz m/z count
+xy_1_1 1 1 1 241 0 22.92 2.48 329.083343505859 0
+xy_2_1 2 1 2 332 0 29.26 2.02 328.916687011719 0
+xy_3_1 3 1 3 415 0 24.43 1.43 328.916687011719 0
+xy_1_2 1 2 4 343 0 39.62 2.59 329 0
+xy_2_2 2 2 5 301 0 18.34 2.38 328.916687011719 0
+xy_3_2 3 2 6 194 0 10.79 1.06 345.083343505859 0
+xy_1_3 1 3 7 308 0 14.68 0.74 328.916687011719 0
+xy_2_3 2 3 8 367 0 24.87 1.33 329 0
+xy_3_3 3 3 9 323 0 35.18 1.73 329.083343505859 0
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessed.rdata
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Binary file test-data/preprocessed.rdata has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results1.RData
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Binary file test-data/preprocessing_results1.RData has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results1.ibd
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Binary file test-data/preprocessing_results1.ibd has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results1.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,313 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{002DF5BA-0549-44DF-A8BB-27DA3E197EB7}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0379019A6F9D0B55F9217420030633F7163AF9D3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spe'..b'ession="IMS:1000050" name="position x" value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="72" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="88" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results1.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results1.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 24
+-rw-r--r-- 1 meli meli    96 Feb 12 21:24 ibd
+-rw-r--r-- 1 meli meli 16714 Feb 12 21:24 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results1.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results1.txt
--- a/test-data/preprocessing_results1.txt Thu Oct 25 07:26:29 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,3 +0,0 @@
-mz x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3
-329 8.48069807321137 6.00276368862812 0 0 7.22240715797167 6.68463797360356 0 0 0
-345 0 0 4.70593890744759 0 0 0 5.23000350586712 4.17949067812964 5.08555910047608
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results2.RData
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results2.ibd
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Binary file test-data/preprocessing_results2.ibd has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results2.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,394 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{84BEACDD-B841-4730-81A0-A19A28C7B48A}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1BC49DCCC566E7A6938CE3DE62090650C2A04798" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="9" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spe'..b'/>\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="42096" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=11" defaultArrayLength="0" index="11">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="46304" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=12" defaultArrayLength="0" index="12">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="50512" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results2.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results2.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 80
+-rw-r--r-- 1 meli meli 54720 Feb 12 21:25 ibd
+-rw-r--r-- 1 meli meli 21132 Feb 12 21:25 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results2.pdf
b
Binary file test-data/preprocessing_results2.pdf has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results2.txt
--- a/test-data/preprocessing_results2.txt Thu Oct 25 07:26:29 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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+++ b/test-data/preprocessing_results3.imzml Fri Feb 15 10:17:43 2019 -0500
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b'@@ -0,0 +1,313 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{4C387879-DE12-49A4-878F-6980D6F7C6F0}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="94ED775BCF16644D23DACFCA1E62D28D5C755178" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spe'..b' value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="9956" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="11376" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="12796" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results3.imzml.txt
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+++ b/test-data/preprocessing_results3.imzml.txt Fri Feb 15 10:17:43 2019 -0500
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@@ -0,0 +1,4 @@
+imzML file:
+total 36
+-rw-r--r-- 1 meli meli 14216 Feb 12 21:26 ibd
+-rw-r--r-- 1 meli meli 16824 Feb 12 21:26 imzml
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results3.pdf
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Binary file test-data/preprocessing_results3.pdf has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results4.RData
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Binary file test-data/preprocessing_results4.RData has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results4.ibd
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Binary file test-data/preprocessing_results4.ibd has changed
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results4.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.imzml Fri Feb 15 10:17:43 2019 -0500
b
b'@@ -0,0 +1,313 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{26018306-9D72-49F5-89CB-68E4DDE0527C}" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="BA6411EC5A5A59ABE5BD7005F4ED8FCEBA775A8E" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="1.12.1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1" />\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="CardinalWriteImzML">\n+\t\t\t<processingMethod order="1" softwareRef="Cardinal">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run defaultInstrumentConfigurationRef="IC1" id="Experiment01" sampleRef="sample1">\n+\t\t<spect'..b'ition x" value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4468" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="5104" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="5740" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results4.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results4.imzml.txt Fri Feb 15 10:17:43 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 28
+-rw-r--r-- 1 meli meli  6376 Feb 12 21:29 ibd
+-rw-r--r-- 1 meli meli 16801 Feb 12 21:29 imzml
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results4.pdf
b
Binary file test-data/preprocessing_results4.pdf has changed
b
diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results4.txt
--- a/test-data/preprocessing_results4.txt Thu Oct 25 07:26:29 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,160 +0,0 @@\n-mz\tx = 1, y = 1\tx = 2, y = 1\tx = 3, y = 1\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 2\tx = 1, y = 3\tx = 2, y = 3\tx = 3, y = 3\n-1199\t1.90173968313755\t1.13259535967648\t2.08382650993109\t2.34349737625869\t1.33087314662273\t2.14468085106383\t3.43161925601751\t1.32706902782797\t2.22480967308554\n-1200\t1.39388874502695\t0.970046951574763\t1.52152411836238\t1.35619061126081\t1.10906095551895\t1.66382978723404\t2.22846006564551\t1.19804842790025\t1.7089117778773\n-1201\t1.13095882671438\t0.99102093971692\t1.23623834616944\t1.19344773790952\t1.05864909390445\t1.31063829787234\t1.67396061269147\t1.07824358511023\t1.28168383340797\n-1202\t1.09263589067539\t0.976548887898831\t1.13518929874341\t1.0033640618352\t0.953389126853377\t1.08663829787234\t1.32242888402626\t0.9820310805927\t1.04469323779669\n-1203\t1.10574636879399\t0.91761198121937\t1.07498986623429\t0.954758190327613\t0.902372322899506\t1.05106382978723\t1.17525984682713\t1.05059631369715\t1.11240483654277\n-1204\t1.06972857176487\t0.959559957503684\t1.0088366436968\t1.01262232307474\t0.972948929159802\t1.02127659574468\t1.20315919037199\t0.972262378026744\t1.04388714733542\n-1205\t0.994091198003719\t0.970046951574763\t1.02537494933117\t0.954758190327613\t0.983031301482702\t1.08936170212766\t1.08807439824945\t0.976870256595591\t0.931034482758621\n-1206\t0.886037806916359\t0.970046951574763\t0.955087150385083\t0.972840731811091\t0.947742998352554\t0.94468085106383\t1.05320021881838\t1.00912540657752\t0.959247648902821\n-1207\t1.05171967325031\t0.933342472325988\t1.01297122010539\t0.93305914054744\t0.917495881383855\t0.982978723404255\t1.00786378555799\t0.972262378026744\t0.983430362740708\n-1208\t1.00489653711246\t0.959559957503684\t1.04604783137414\t0.994539781591264\t1.00823723228995\t1.01276595744681\t1.05668763676149\t0.999909649439827\t0.991491267353336\n-1209\t1.34346382918619\t1.15356934781864\t1.26518038102959\t1.31640901999716\t1.0737726523888\t1.20425531914894\t1.19269693654267\t1.23951933501988\t1.12449619346171\n-1210\t1.2413173568116\t1.11749408821413\t1.25029590595865\t1.25333711530279\t1.12277298187809\t1.0743829787234\t1.08472647702407\t1.13685580050596\t1.07564711150918\n-1211\t1.12375526730855\t0.98577744268138\t1.09152817186867\t1.05240391433839\t0.967907742998353\t1.07659574468085\t0.997401531728665\t1.07824358511023\t1.07613076578594\n-1212\t1.05892323265614\t1.04869940710785\t0.979894608836644\t1.00900581477805\t0.993113673805601\t1\t0.979964442013129\t1.04138055655945\t1.06806986117331\n-1213\t0.990489418300808\t0.996264436752459\t1.0088366436968\t1.03432137285491\t1.01831960461285\t0.987234042553191\t0.986939277899344\t1.02294904228406\t1.08419167039857\n-1214\t1.07333035146778\t0.875664004935056\t1.06258613700851\t1.05240391433839\t0.967907742998353\t1.02127659574468\t1.0601750547046\t1.02294904228406\t1.08822212270488\n-1215\t1.15256950493185\t0.964803454539223\t1.11633563032023\t1.07048645582187\t1.0939373970346\t1.17021276595745\t1.13689824945295\t1.08745934224792\t1.205105239588\n-1216\t1.05532145295322\t0.98577744268138\t1.12873935954601\t1.02708835626152\t1.0031960461285\t1.08936170212766\t1.13341083150985\t1.04138055655945\t1.08419167039857\n-1217\t0.950869841568775\t0.975290448610302\t0.959221726793677\t0.961991206921004\t1.02840197693575\t0.970212765957447\t0.955552516411379\t0.972262378026744\t1.01970443349754\n-1218\t0.943666282162951\t0.970046951574763\t0.959221726793677\t0.9656077152177\t0.932619439868204\t0.906382978723404\t0.927653172866521\t1.05981207083484\t1.00761307657859\n-1219\t0.860825348995975\t0.933342472325988\t0.984029185245237\t0.969224223514395\t0.927578253706755\t0.957446808510638\t0.892778993435449\t0.944615106613661\t0.96730855351545\n-1220\t0.929259163351303\t0.938585969361527\t1.00056749087961\t0.889661040987094\t0.962866556836903\t1.00425531914894\t1.07761214442013\t0.986086013733285\t1.08016121809225\n-1221\t0.997692977706632\t0.975290448610302\t0.971625456019457\t0.940292157140831\t0.942701812191104\t1.0936170212766\t1.27290754923414\t1.08745934224792\t1.12449619346171\n-1222\t0.983285858894983\t0.975290448610302\t0.946817997567896\t0.918593107360658\t0.942701812191104\t1.05106382978723\t1.13689824945295\t1.0459884351283\t1.0237348858038'..b'1.02198251523589\n-1333\t1.07113796382253\t1.17089568584911\t1.04407042526568\t1.14721932750828\t1.0625943700308\t1.06123959296947\t1.05168395014746\t1.06261686648544\t1.026188204599\n-1334\t1.0297957967978\t1.08335208316881\t0.923268888458081\t1.08683936290258\t0.98894921567223\t0.981313598519889\t1.03712777090667\t1.0001099919863\t0.950485796063007\n-1335\t0.988453629773075\t0.957508154315864\t0.931897569658624\t0.913246964661195\t0.941605902156006\t0.945790934320074\t0.887926933688517\t0.995301770870979\t0.946280106699897\n-1336\t0.871943886339746\t0.935622253645788\t0.811096032851025\t0.886830730146202\t0.925824797650598\t0.941350601295097\t0.902483112929312\t0.971260665294386\t0.963102864152339\n-1337\t0.860668749878457\t0.979394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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results5.RData
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results5.pdf
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/preprocessing_results5.txt
--- a/test-data/preprocessing_results5.txt Thu Oct 25 07:26:29 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,100 +0,0 @@
- x = 1, y = 1 x = 2, y = 1 x = 3, y = 1 x = 1, y = 2 x = 2, y = 2 x = 3, y = 2 x = 1, y = 3 x = 2, y = 3 x = 3, y = 3
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diff -r 65ef413a35f3 -r e30d8b72415f test-data/scores_pca.tabular
--- a/test-data/scores_pca.tabular Thu Oct 25 07:26:29 2018 -0400
+++ b/test-data/scores_pca.tabular Fri Feb 15 10:17:43 2019 -0500
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@@ -1,10 +1,10 @@
 pixel names x y PC1 PC2
-xy_1_1 1 1 1.00970093989579 0.757987492163095
-xy_2_1 2 1 0.579669229309751 -0.365615195586663
-xy_3_1 3 1 -1.04790449059337 0.831141108678224
-xy_1_2 1 2 3.5004093695087 0.608578545994517
-xy_2_2 2 2 -0.325050824762022 0.275854508943195
-xy_3_2 3 2 -1.31374997886227 0.0192699346592569
-xy_1_3 1 3 -1.46193831394872 -0.0337353199555284
-xy_2_3 2 3 -1.08833133183905 1.16461090511219
-xy_3_3 3 3 0.147195401291175 -3.25809198000829
+xy_1_1 1 1 1.009701 0.757987
+xy_2_1 2 1 0.579669 -0.365615
+xy_3_1 3 1 -1.047904 0.831141
+xy_1_2 1 2 3.500409 0.608579
+xy_2_2 2 2 -0.325051 0.275855
+xy_3_2 3 2 -1.31375 0.01927
+xy_1_3 1 3 -1.461938 -0.033735
+xy_2_3 2 3 -1.088331 1.164611
+xy_3_3 3 3 0.147195 -3.258092
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