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

Changeset 7:4a2ac25d1063 (2020-04-23)
Previous changeset 6:82f6c2f4332d (2020-03-25) Next changeset 8:b591450b3d1c (2020-05-13)
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
modified:
macros.xml
segmentation.xml
test-data/112_auto_combined.imzml
test-data/112_auto_combined.imzml.txt
test-data/112_auto_combined_QC.pdf
test-data/123_combined.imzml
test-data/123_combined.imzml.txt
test-data/123_combined_QC.pdf
test-data/123_combined_auto.imzml
test-data/123_combined_auto.imzml.txt
test-data/123_combined_auto.pdf
test-data/12_combined.imzml
test-data/12_combined.imzml.txt
test-data/12_combined_QC.pdf
test-data/2123_auto_combined.imzml
test-data/2123_auto_combined.imzml.txt
test-data/2123_auto_combined_QC.pdf
test-data/Heatmaps_LM8_file16.pdf
test-data/Heatmaps_analyze75.pdf
test-data/Heatmaps_imzml.pdf
test-data/Heatmaps_rdata.pdf
test-data/Plot_analyze75.pdf
test-data/Plot_analyze75_allpixels.pdf
test-data/Plot_imzml.pdf
test-data/Plot_rdata.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.svg
test-data/centroids_rdata.pdf
test-data/classes_ssc.tabular
test-data/cluster_skm.RData
test-data/cluster_skm.tabular
test-data/features_out1.tabular
test-data/features_out3.tabular
test-data/features_test6.tabular
test-data/int_matrix1.tabular
test-data/int_matrix3.tabular
test-data/kmeans_analyze.pdf
test-data/mean_out2.tabular
test-data/pca_imzml.pdf
test-data/picked.ibd
test-data/picked.imzml
test-data/picked.imzml.txt
test-data/picked_QC.pdf
test-data/pixel_out3.tabular
test-data/pixels_test6.tabular
test-data/preprocessing_results3.ibd
test-data/preprocessing_results3.imzml
test-data/preprocessing_results3.imzml.txt
test-data/preprocessing_results3.pdf
test-data/preprocessing_results5.ibd
test-data/preprocessing_results5.imzml
test-data/preprocessing_results5.imzml.txt
test-data/preprocessing_results5.pdf
test-data/sd_out2.tabular
test-data/test6.pdf
test-data/test6.rdata
test-data/toplabels_skm.tabular
test-data/toplabels_ssc.tabular
added:
test-data/Heatmaps_processed.pdf
test-data/Plot_picked.pdf
test-data/Plot_processed.pdf
test-data/centroids_proc.pdf
test-data/classes_proc.tabular
test-data/features_out4.tabular
test-data/pixel_out4.tabular
test-data/spectra_1_pixel.tabular
test-data/toplabels_proc.tabular
removed:
test-data/Plot_empty_spectra.pdf
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 macros.xml
--- a/macros.xml Wed Mar 25 05:43:05 2020 -0400
+++ b/macros.xml Thu Apr 23 08:09:32 2020 -0400
[
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@VERSION@">1.12.1</token>
+    <token name="@VERSION@">2.4.0</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>
-            <requirement type="package" version="3.5.1">r-base</requirement>
+            <requirement type="package" version="3.6.1">r-base</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -32,15 +32,10 @@
     <token name="@READING_MSIDATA@"><![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", attach.only=TRUE)
+                msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units")
+                msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous
                 centroided(msidata) = $centroids
             #else
                 msidata <- readImzML('infile', attach.only=TRUE)
@@ -50,6 +45,11 @@
             msidata = readAnalyze('infile', attach.only=TRUE)
             centroided(msidata) = $centroids
         #else
+            ## function to read RData files independent of filename
+            loadRData <- function(fileName){
+            load(fileName)
+            get(ls()[ls() != "fileName"])
+            }
             msidata = loadRData('infile.RData')
         #end if
 
@@ -86,34 +86,34 @@
         property_df = data.frame(properties, values)
     ]]></token>
 
-    <token name="@READING_MSIDATA_INRAM@"><![CDATA[
+    <token name="@READING_MSIDATA_FULLY_COMPATIBLE@"><![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")
+                msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
                 centroided(msidata) = $centroids
-                iData(msidata) = iData(msidata)[]
             #else
-                msidata <- readImzML('infile')
+                msidata <- readImzML('infile', attach.only=TRUE)
                 centroided(msidata) = $centroids
             #end if
         #elif $infile.ext == 'analyze75'
-            msidata = readAnalyze('infile')
+            msidata = readAnalyze('infile', attach.only=TRUE)
             centroided(msidata) = $centroids
         #else
+            ## function to read RData files independent of filename
+            loadRData <- function(fileName){
+            load(fileName)
+            get(ls()[ls() != "fileName"])
+            }
             msidata = loadRData('infile.RData')
+            msidata = as(msidata, "MSImagingExperiment")
+            run(msidata) = "infile"
         #end if
 
     ]]></token>
 
-    <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[
+    <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ 
 ########################### QC numbers ########################
 ## including intensity calculations which need data in RAM
         ## Number of features (mz)
@@ -130,17 +130,16 @@
         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)
+        minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
+        maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
         ## Number of intensities > 0, for if conditions
-        npeaks= sum(spectra(msidata)>0, na.rm=TRUE)
+        npeaks= sum(as.matrix(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)))
+        infcount = sum(is.infinite(as.matrix(spectra(msidata))))
         ## Number of duplicated coordinates
         dupl_coord = sum(duplicated(coord(msidata)))
-
         properties = c("Number of m/z features",
                        "Range of m/z values",
                        "Number of pixels", 
@@ -298,6 +297,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/bioinformatics/btv146</citation>
+            <citation type="doi">10.1093/gigascience/giz143</citation>
         </citations>
     </xml>
     <xml name="infile_analyze75">
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 segmentation.xml
--- a/segmentation.xml Wed Mar 25 05:43:05 2020 -0400
+++ b/segmentation.xml Thu Apr 23 08:09:32 2020 -0400
[
b'@@ -1,12 +1,11 @@\n-<tool id="cardinal_segmentations" name="MSI segmentation" version="@VERSION@.3">\n+<tool id="cardinal_segmentations" name="MSI segmentation" version="@VERSION@.0">\n     <description>mass spectrometry imaging spatial clustering</description>\n     <macros>\n         <import>macros.xml</import>\n     </macros>\n     <expand macro="requirements">\n         <requirement type="package" version="2.3">r-gridextra</requirement>\n-        <requirement type="package" version="0.20_35">r-lattice</requirement>\n-    </expand>\n+      </expand>\n     <command detect_errors="exit_code">\n     <![CDATA[\n \n@@ -19,17 +18,14 @@\n     <configfiles>\n         <configfile name="MSI_segmentation"><![CDATA[\n \n-\n ################################# load libraries and read file #################\n \n library(Cardinal)\n library(gridExtra)\n-library(lattice)\n-\n \n+@READING_MSIDATA@\n \n-@READING_MSIDATA_INRAM@\n-\n+       msidata = as(msidata, "MSImageSet") ##coercion to MSImageSet\n \n ## remove duplicated coordinates\n msidata <- msidata[,!duplicated(coord(msidata))]\n@@ -61,21 +57,6 @@\n         #set $color_string = \',\'.join([\'"%s"\' % $color.feature_color for $color in $colours])\n         colourvector = c($color_string)\n \n-        ### preparation for images and plots:\n-        #if str($image_type) == "standard_image":\n-            print("standard image")\n-\n-            strip_input = FALSE\n-            lattice_input = FALSE\n-\n-        #elif str($image_type) == "lattice_image":\n-            print("lattice image")\n-\n-            strip_input = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9))\n-            lattice_input = TRUE\n-\n-        #end if\n-\n         ## set seed to make analysis reproducible\n         set.seed($setseed)\n \n@@ -105,11 +86,11 @@\n             colnames(sd_table)[1] = "Principal components"\n             grid.table(sd_table, rows=NULL)\n             ### images in pdf file\n-            print(image(pca_result, main="PCA image", lattice=lattice_input, strip = strip_input, col=colourvector, ylim=c(maximumy+2, minimumy-2)))\n+            print(image(pca_result, main="PCA image", strip = FALSE, col=colourvector, ylim=c(maximumy+2, minimumy-2)))\n             for (PCs in 1:$segm_cond.pca_ncomp){\n-                print(image(pca_result, column = c(paste0("PC",PCs)), lattice=lattice_input,strip = strip_input, superpose = FALSE, main=paste0("PC", PCs), col.regions = risk.colors(100), ylim=c(maximumy+2, minimumy-2)))}\n+                print(image(pca_result, column = c(paste0("PC",PCs)),strip = FALSE, superpose = FALSE, main=paste0("PC", PCs), col.regions = risk.colors(100), ylim=c(maximumy+2, minimumy-2)))}\n             ### plots in pdf file\n-            print(plot(pca_result, main="PCA plot", lattice=lattice_input, col= colourvector, strip = strip_input))\n+            print(plot(pca_result, main="PCA plot", col= colourvector, strip = FALSE))\n             for (PCs in 1:$segm_cond.pca_ncomp){\n                 print(plot(pca_result, column = c(paste0("PC",PCs)),main=paste0("PC", PCs),strip = FALSE,superpose = FALSE))}\n \n@@ -149,8 +130,8 @@\n             rm(msidata)\n             gc()\n \n-            print(image(skm, key=TRUE, main="K-means clustering", lattice=lattice_input, strip=strip_input, col= colourvector, layout=c(1,1), ylim=c(maximumy+2, minimumy-2)))\n-            print(plot(skm, main="K-means plot", lattice=lattice_input, col= colourvector, strip=strip_input, layout=c(1,1)))\n+            print(image(skm, key=TRUE, main="K-means clustering", strip=FALSE, col= colourvector, layout=c(1,1), ylim=c(maximumy+2, minimumy-2)))\n+            print(plot(skm, main="K-means plot", col= colourvector, strip=FALSE, layout=c(1,1)))\n \n             skm_clusters = data.frame(matrix(NA, nrow = pixelcount, ncol = 0))\n             for (iteration in 1:length(skm@resultData)){\n@@ -167,7 +148,7 @@\n             skm_clusters2 = data.frame(pixel_names, x_coordinates, y_coordinates, skm_clusters)\n             colnames(skm_clusters2) = c("pixel names", "x", "y",names'..b'"\\t")\n@@ -313,8 +294,6 @@\n                        label="Number of toplabels (m/z) which should be written in tabular output"/>\n                 </when>\n             </conditional>\n-            <param name="image_type" type="boolean" checked="True" truevalue="standard_image" falsevalue="lattice_image" \n-            label="Standard image" help="No: lattice function is used to display image"/>\n             <param name="svg_pixelimage" type="boolean" label="Export first segmentation image as svg"/>\n             <repeat name="colours" title="Colours for the plots" min="1" max="50">\n                 <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of components">\n@@ -343,7 +322,6 @@\n         <test>\n             <expand macro="infile_imzml"/>\n             <param name="segmentationtool" value="pca"/>\n-            <param name="image_type" value="lattice_image"/>\n             <repeat name="colours">\n                 <param name="feature_color" value="#ff00ff"/>\n             </repeat>\n@@ -353,7 +331,8 @@\n             <output name="segmentationimages" file="pca_imzml.pdf" compare="sim_size"/>\n             <output name="mzfeatures">\n                 <assert_contents>\n-                    <has_text text="300.17" />\n+                    <has_text text="300.1667" />\n+                    <has_text text="300.25" />\n                     <has_text text="-4.234458e-04" />\n                     <has_text text="3.878545e-10" />\n                     <has_n_columns n="3" />\n@@ -362,7 +341,7 @@\n             <output name="pixeloutput" file="scores_pca.tabular"/>\n         </test>\n         <test>\n-            <expand macro="infile_analyze75"/>\n+            <expand macro="infile_imzml"/>\n             <param name="segmentationtool" value="kmeans"/>\n             <param name="kmeans_r" value="1:3"/>\n             <param name="kmeans_k" value="2,3"/>\n@@ -397,16 +376,38 @@\n             <repeat name="colours">\n                 <param name="feature_color" value="#B0171F"/>\n             </repeat>\n-            <repeat name="colours">\n-                <param name="feature_color" value="#FFD700"/>\n-            </repeat>\n-            <repeat name="colours">\n-                <param name="feature_color" value="#848484"/>\n-            </repeat>\n             <output name="segmentationimages" file="centroids_rdata.pdf" compare="sim_size"/>\n             <output name="mzfeatures" file="toplabels_ssc.tabular"/>\n             <output name="pixeloutput" file="classes_ssc.tabular"/>\n         </test>\n+        <test>\n+            <param name="infile" value="" ftype="imzml">\n+                <composite_data value="preprocessing_results3.imzml"/>\n+                <composite_data value="preprocessing_results3.ibd"/>\n+            </param>\n+            <conditional name="processed_cond">\n+                <param name="processed_file" value="processed"/>\n+                <param name="accuracy" value="1"/>\n+                <param name="units" value="mz"/>\n+            </conditional>\n+            <param name="segmentationtool" value="centroids"/>\n+            <param name="centroids_r" value="1"/>\n+            <param name="centroids_k" value="2,3"/>\n+            <param name="centroids_s" value="0,3"/>\n+            <param name="centroids_toplabels" value="100"/>\n+            <repeat name="colours">\n+                <param name="feature_color" value="#0000FF"/>\n+            </repeat>\n+            <repeat name="colours">\n+                <param name="feature_color" value="#00C957"/>\n+            </repeat>\n+            <repeat name="colours">\n+                <param name="feature_color" value="#B0171F"/>\n+            </repeat>\n+            <output name="segmentationimages" file="centroids_proc.pdf" compare="sim_size"/>\n+            <output name="mzfeatures" file="toplabels_proc.tabular"/>\n+            <output name="pixeloutput" file="classes_proc.tabular"/>\n+        </test>\n     </tests>\n     <help>\n         <![CDATA[\n'
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/112_auto_combined.imzml
--- a/test-data/112_auto_combined.imzml Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/112_auto_combined.imzml Thu Apr 23 08:09:32 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="a0620366-fee2-4a2a-a643-0f0e0c9ae5a6" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bcd78ace1e6441dc527501b5eb3994fcf15b894" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="de720b1f-c3fa-4596-b054-284efaff29fc" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="040b9782d76e25ebe9a6b7c27fdda7e27e711674" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -42,7 +42,7 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="2.2.6">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
@@ -78,6 +78,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -105,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -132,6 +136,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -159,6 +165,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -186,6 +194,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -213,6 +223,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -240,6 +252,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="9.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -267,6 +281,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="10" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="10.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -294,6 +310,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="9.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -321,6 +339,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="10" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="10.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -348,6 +368,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="9.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -375,6 +397,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="10" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="10.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -402,6 +426,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="15" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="15.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -429,6 +455,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="15" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="15.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -456,6 +484,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="15" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="15.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/112_auto_combined.imzml.txt
--- a/test-data/112_auto_combined.imzml.txt Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/112_auto_combined.imzml.txt Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 556
--rw-r--r-- 1 meli meli 537552 Dez 11 00:10 ibd
--rw-r--r-- 1 meli meli  25811 Dez 11 00:10 imzml
+-rw-r--r-- 1 meli meli 537552 Apr 21 12:46 ibd
+-rw-r--r-- 1 meli meli  27497 Apr 21 12:46 imzml
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/112_auto_combined_QC.pdf
b
Binary file test-data/112_auto_combined_QC.pdf has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/123_combined.imzml
--- a/test-data/123_combined.imzml Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/123_combined.imzml Thu Apr 23 08:09:32 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="8421b4d5-42be-4040-9d94-0398a40d6121" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d2cf2df8db9b95afd23834703bc933df1098bb6d" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c9f19079-a92c-4995-b4ee-48d2766994a8" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="889b1020d3d844330f13a360be4b2bd0b65d11a1" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -42,7 +42,7 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="2.2.6">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
@@ -78,6 +78,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -105,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -132,6 +136,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -159,6 +165,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -186,6 +194,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="4" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="4.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -213,6 +223,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -240,6 +252,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="4" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="4.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -267,6 +281,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -294,6 +310,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="4" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="4.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -321,6 +339,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="9.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -348,6 +368,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="9.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -375,6 +397,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="9.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/123_combined.imzml.txt
--- a/test-data/123_combined.imzml.txt Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/123_combined.imzml.txt Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 452
--rw-r--r-- 1 meli meli 436764 Dez 11 00:02 ibd
--rw-r--r-- 1 meli meli  21511 Dez 11 00:02 imzml
+-rw-r--r-- 1 meli meli 436764 Apr 21 12:41 ibd
+-rw-r--r-- 1 meli meli  22855 Apr 21 12:41 imzml
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/123_combined_QC.pdf
b
Binary file test-data/123_combined_QC.pdf has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/123_combined_auto.imzml
--- a/test-data/123_combined_auto.imzml Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/123_combined_auto.imzml Thu Apr 23 08:09:32 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c12d4d26-5ff1-4c3c-99ea-95e0858faf36" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="147d6aa7f71a366246c93d750fcc9240b84c748f" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="386d1a7c-e065-4bf1-96a6-019586133b29" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bdafd878211e7d0c8fd0ef11bd534cbacfe7d40" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -42,7 +42,7 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="2.2.6">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
@@ -78,6 +78,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -105,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -132,6 +136,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -159,6 +165,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -186,6 +194,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="8.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -213,6 +223,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -240,6 +252,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="8.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -267,6 +281,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -294,6 +310,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="8.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -321,6 +339,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="9" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="9.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -348,6 +368,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="10" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="10.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -375,6 +397,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="11" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="11.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/123_combined_auto.imzml.txt
--- a/test-data/123_combined_auto.imzml.txt Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/123_combined_auto.imzml.txt Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 452
--rw-r--r-- 1 meli meli 436764 Dez 11 00:05 ibd
--rw-r--r-- 1 meli meli  21514 Dez 11 00:05 imzml
+-rw-r--r-- 1 meli meli 436764 Apr 21 12:43 ibd
+-rw-r--r-- 1 meli meli  22860 Apr 21 12:43 imzml
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/123_combined_auto.pdf
b
Binary file test-data/123_combined_auto.pdf has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/12_combined.imzml
--- a/test-data/12_combined.imzml Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/12_combined.imzml Thu Apr 23 08:09:32 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="e9aca5c3-32c8-416b-a9e9-e40ba239ce32" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c0c53177dc3a008c7a18ba10fe139ccaecc295a2" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="57f26041-833d-4843-ba25-0037f2c35f51" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c271b37214900da9960cd3bcb748cc5bc377cfec" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -42,7 +42,7 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="2.2.6">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
@@ -78,6 +78,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -105,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -132,6 +136,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -159,6 +165,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -186,6 +194,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="8.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -213,6 +223,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -240,6 +252,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="8.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -267,6 +281,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="7.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -294,6 +310,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="8.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/12_combined.imzml.txt
--- a/test-data/12_combined.imzml.txt Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/12_combined.imzml.txt Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 352
--rw-r--r-- 1 meli meli 335976 Dez 11 00:07 ibd
--rw-r--r-- 1 meli meli  17217 Dez 11 00:07 imzml
+-rw-r--r-- 1 meli meli 335976 Apr 21 12:45 ibd
+-rw-r--r-- 1 meli meli  18225 Apr 21 12:45 imzml
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/12_combined_QC.pdf
b
Binary file test-data/12_combined_QC.pdf has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/2123_auto_combined.imzml
--- a/test-data/2123_auto_combined.imzml Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/2123_auto_combined.imzml Thu Apr 23 08:09:32 2020 -0400
b
b'@@ -9,8 +9,8 @@\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="89a84e82-79bf-466a-a1ce-e942e7cfe37d" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5d2027d8c0ad315ac09a1c7c4edf84d3d4facd90" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="1c0a127a-8417-47ef-a049-553b9d56de81" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5113bf7d09e0b1a584238aa6c5242f50eeef839b" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -42,7 +42,7 @@\n \t\t</sample>\n \t</sampleList>\n \t<softwareList count="1">\n-\t\t<software id="Cardinal" version="2.2.6">\n+\t\t<software id="Cardinal" version="2.4.0">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n \t\t</software>\n \t</softwareList>\n@@ -78,6 +78,8 @@\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="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="1.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -105,6 +107,8 @@\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="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="2.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -132,6 +136,8 @@\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="2" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="1.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="2.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -159,6 +165,8 @@\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\t<userParam name="3DPositionX" value="2.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="2.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -186,6 +194,8 @@\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\t<userParam name="3DPositionX" value="1.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -213,6 +223,8 @@\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\t<userParam name="3DPositionX" value="2.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -240,6 +252,8 @@\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="8" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="8.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t'..b'0051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="8.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -321,6 +339,8 @@\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="10" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="10.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -348,6 +368,8 @@\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="11" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="11.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -375,6 +397,8 @@\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="10" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="10.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="2.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -402,6 +426,8 @@\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="11" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="11.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="2.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -429,6 +455,8 @@\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="10" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="10.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -456,6 +484,8 @@\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="11" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="11.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -483,6 +513,8 @@\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="16" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="16.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -510,6 +542,8 @@\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="16" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="16.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="2.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n@@ -537,6 +571,8 @@\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="16" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="16.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n'
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/2123_auto_combined.imzml.txt
--- a/test-data/2123_auto_combined.imzml.txt Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/2123_auto_combined.imzml.txt Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 656
--rw-r--r-- 1 meli meli 638340 Dez 11 00:12 ibd
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diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/analyze75.svg
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diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/features_out1.tabular
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b
b'@@ -1,1200 +1,1200 @@\n mz_names\tmz\tsample_mean\tsample_median\tsample_sd\tsample_sem\tintensity_sum\tnumber_peaks\n-mz_300.08\t300.083343505859\t0.0292992062038845\t0\t0.0878976186116536\t300\t0.263692855834961\t1\n-mz_300.17\t300.166687011719\t0.00287774681217141\t0\t0.00863324043651422\t300\t0.0258997213095427\t1\n+mz_300.083343505859\t300.083343505859\t0.0292992062038845\t0\t0.0878976186116536\t300\t0.263692855834961\t1\n+mz_300.166687011719\t300.166687011719\t0.00287774681217141\t0\t0.00863324043651422\t300\t0.0258997213095427\t1\n mz_300.25\t300.25\t1.77280128848483e-10\t0\t5.31840386545449e-10\t300\t1.59552115963635e-09\t1\n-mz_300.33\t300.333343505859\t5.14883475361611e-11\t0\t1.54465042608483e-10\t300\t4.6339512782545e-10\t1\n-mz_300.42\t300.416687011719\t4.0139211399115e-12\t0\t1.20417634197345e-11\t300\t3.61252902592035e-11\t1\n+mz_300.333343505859\t300.333343505859\t5.14883475361611e-11\t0\t1.54465042608483e-10\t300\t4.6339512782545e-10\t1\n+mz_300.416687011719\t300.416687011719\t4.0139211399115e-12\t0\t1.20417634197345e-11\t300\t3.61252902592035e-11\t1\n mz_300.5\t300.5\t5.50704215937811e-06\t0\t1.65211264781343e-05\t300\t4.9563379434403e-05\t1\n-mz_300.58\t300.583343505859\t3.95111985401147e-06\t0\t1.18533595620344e-05\t300\t3.55600786861032e-05\t1\n-mz_300.67\t300.666687011719\t7.27397238935939e-07\t0\t2.18219171680782e-06\t300\t6.54657515042345e-06\t1\n+mz_300.583343505859\t300.583343505859\t3.95111985401147e-06\t0\t1.18533595620344e-05\t300\t3.55600786861032e-05\t1\n+mz_300.666687011719\t300.666687011719\t7.27397238935939e-07\t0\t2.18219171680782e-06\t300\t6.54657515042345e-06\t1\n mz_300.75\t300.75\t1.30250899042089e-14\t0\t3.90752697126268e-14\t300\t1.1722580913788e-13\t1\n-mz_300.83\t300.833343505859\t7.27670494871757e-15\t0\t2.18301148461527e-14\t300\t6.54903445384582e-14\t1\n-mz_300.92\t300.916687011719\t1.19033973005598e-15\t0\t3.57101919016793e-15\t300\t1.07130575705038e-14\t1\n+mz_300.833343505859\t300.833343505859\t7.27670494871757e-15\t0\t2.18301148461527e-14\t300\t6.54903445384582e-14\t1\n+mz_300.916687011719\t300.916687011719\t1.19033973005598e-15\t0\t3.57101919016793e-15\t300\t1.07130575705038e-14\t1\n mz_301\t301\t0\t0\t0\tNA\t0\t0\n-mz_301.08\t301.083343505859\t4.24474381569932e-10\t0\t1.2734231447098e-09\t300\t3.82026943412939e-09\t1\n-mz_301.17\t301.166687011719\t1.2672437173696e-10\t0\t3.8017311521088e-10\t300\t1.14051934563264e-09\t1\n+mz_301.083343505859\t301.083343505859\t4.24474381569932e-10\t0\t1.2734231447098e-09\t300\t3.82026943412939e-09\t1\n+mz_301.166687011719\t301.166687011719\t1.2672437173696e-10\t0\t3.8017311521088e-10\t300\t1.14051934563264e-09\t1\n mz_301.25\t301.25\t1.04927193477088e-11\t0\t3.14781580431263e-11\t300\t9.4434474129379e-11\t1\n-mz_301.33\t301.333343505859\t8.29418595654768e-19\t0\t2.4882557869643e-18\t300\t7.46476736089292e-18\t1\n-mz_301.42\t301.416687011719\t2.20798332887492e-19\t0\t6.62394998662477e-19\t300\t1.98718499598743e-18\t1\n+mz_301.333343505859\t301.333343505859\t8.29418595654768e-19\t0\t2.4882557869643e-18\t300\t7.46476736089292e-18\t1\n+mz_301.416687011719\t301.416687011719\t2.20798332887492e-19\t0\t6.62394998662477e-19\t300\t1.98718499598743e-18\t1\n mz_301.5\t301.5\t1.36295095239794e-20\t0\t4.08885285719383e-20\t300\t1.22665585715815e-19\t1\n-mz_301.58\t301.583343505859\t3.00898357879359e-14\t0\t9.02695073638077e-14\t300\t2.70808522091423e-13\t1\n-mz_301.67\t301.666687011719\t1.77132674365446e-14\t0\t5.31398023096337e-14\t300\t1.59419406928901e-13\t1\n+mz_301.583343505859\t301.583343505859\t3.00898357879359e-14\t0\t9.02695073638077e-14\t300\t2.70808522091423e-13\t1\n+mz_301.666687011719\t301.666687011719\t1.77132674365446e-14\t0\t5.31398023096337e-14\t300\t1.59419406928901e-13\t1\n mz_301.75\t301.75\t2.98124144276739e-15\t0\t8.94372432830217e-15\t300\t2.68311729849065e-14\t1\n-mz_301.83\t301.833343505859\t6.7355936850742e-23\t0\t2.02067810552226e-22\t300\t6.06203431656678e-22\t1\n-mz_301.92\t301.916687011719\t3.23492041045198e-23\t0\t9.70476123135593e-23\t300\t2.91142836940678e-22\t1\n+mz_301.833343505859\t301.833343505859\t6.7355936850742e-23\t0\t2.02067810552226e-22\t300\t6.06203431656678e-22\t1\n+mz_301.916687011719\t301.916687011719\t3.23492041045198e-23\t0\t9.70476123135593e-23\t300\t2.91142836940678e-22\t1\n mz_302\t302\t4.80219917504923e-24\t0\t1.440659752'..b'87e-07\t300\t4.5503847445616e-07\t2\n-mz_397.92\t397.916687011719\t2.1973092932285e-23\t0\t6.59192787967557e-23\t299.999999999548\t1.97757836390565e-22\t2\n+mz_397.833343505859\t397.833343505859\t5.05598304951289e-08\t0\t1.51679491485387e-07\t300\t4.5503847445616e-07\t2\n+mz_397.916687011719\t397.916687011719\t2.1973092932285e-23\t0\t6.59192787967557e-23\t299.999999999548\t1.97757836390565e-22\t2\n mz_398\t398\t3.04395583748723e-24\t0\t9.13186751242318e-24\t299.999999998735\t2.73956025373851e-23\t2\n-mz_398.08\t398.083343505859\t0.00435541777147187\t0\t0.0130662533144156\t300\t0.0391987599432468\t3\n-mz_398.17\t398.166687011719\t0.0476158229749465\t0\t0.142847468396982\t299.999998891423\t0.428542406774519\t3\n+mz_398.083343505859\t398.083343505859\t0.00435541777147187\t0\t0.0130662533144156\t300\t0.0391987599432468\t3\n+mz_398.166687011719\t398.166687011719\t0.0476158229749465\t0\t0.142847468396982\t299.999998891423\t0.428542406774519\t3\n mz_398.25\t398.25\t0.0337751011944952\t0\t0.101325303282695\t299.999999109431\t0.303975910750457\t3\n-mz_398.33\t398.333343505859\t0.00567932097266618\t0\t0.017037962868249\t299.999999124024\t0.0511138887539956\t2\n-mz_398.42\t398.416687011719\t0\t0\t0\tNA\t0\t0\n+mz_398.333343505859\t398.333343505859\t0.00567932097266618\t0\t0.017037962868249\t299.999999124024\t0.0511138887539956\t2\n+mz_398.416687011719\t398.416687011719\t0\t0\t0\tNA\t0\t0\n mz_398.5\t398.5\t1.45001195853997e-39\t0\t4.35003587561991e-39\t300\t1.30501076268597e-38\t1\n-mz_398.58\t398.583343505859\t5.86734578455249e-32\t0\t1.76020373536575e-31\t300\t5.28061120609724e-31\t1\n-mz_398.67\t398.666687011719\t0.00365118661688434\t0\t0.0075229081301236\t206.040088319099\t0.032860679551959\t3\n+mz_398.583343505859\t398.583343505859\t5.86734578455249e-32\t0\t1.76020373536575e-31\t300\t5.28061120609724e-31\t1\n+mz_398.666687011719\t398.666687011719\t0.00365118661688434\t0\t0.0075229081301236\t206.040088319099\t0.032860679551959\t3\n mz_398.75\t398.75\t0.0974471403492822\t0\t0.218609809238247\t224.336813224769\t0.877024263143539\t3\n-mz_398.83\t398.833343505859\t0.0827518999576569\t0\t0.185963341513219\t224.723953901208\t0.744767099618912\t3\n-mz_398.92\t398.916687011719\t0.0164484298891491\t0\t0.037280611765694\t226.651492069086\t0.148035869002342\t2\n+mz_398.833343505859\t398.833343505859\t0.0827518999576569\t0\t0.185963341513219\t224.723953901208\t0.744767099618912\t3\n+mz_398.916687011719\t398.916687011719\t0.0164484298891491\t0\t0.037280611765694\t226.651492069086\t0.148035869002342\t2\n mz_399\t399\t0\t0\t0\tNA\t0\t0\n-mz_399.08\t399.083343505859\t0\t0\t0\tNA\t0\t0\n-mz_399.17\t399.166687011719\t2.12591405853366e-35\t0\t6.37774217560099e-35\t300\t1.9133226526803e-34\t1\n+mz_399.083343505859\t399.083343505859\t0\t0\t0\tNA\t0\t0\n+mz_399.166687011719\t399.166687011719\t2.12591405853366e-35\t0\t6.37774217560099e-35\t300\t1.9133226526803e-34\t1\n mz_399.25\t399.25\t8.92074257340149e-36\t0\t2.67622277202045e-35\t300\t8.02866831606135e-35\t1\n-mz_399.33\t399.333343505859\t8.50251995466857e-06\t0\t1.90083935605297e-05\t223.561881205496\t7.65226795920171e-05\t3\n-mz_399.42\t399.416687011719\t2.75656642164298e-06\t0\t6.22119222208426e-06\t225.686280339158\t2.48090977947868e-05\t2\n+mz_399.333343505859\t399.333343505859\t8.50251995466857e-06\t0\t1.90083935605297e-05\t223.561881205496\t7.65226795920171e-05\t3\n+mz_399.416687011719\t399.416687011719\t2.75656642164298e-06\t0\t6.22119222208426e-06\t225.686280339158\t2.48090977947868e-05\t2\n mz_399.5\t399.5\t2.66098109275643e-07\t0\t6.10309301715427e-07\t229.354993681382\t2.39488298348078e-06\t2\n-mz_399.58\t399.583343505859\t0\t0\t0\tNA\t0\t0\n-mz_399.67\t399.666687011719\t0\t0\t0\tNA\t0\t0\n+mz_399.583343505859\t399.583343505859\t0\t0\t0\tNA\t0\t0\n+mz_399.666687011719\t399.666687011719\t0\t0\t0\tNA\t0\t0\n mz_399.75\t399.75\t0\t0\t0\tNA\t0\t0\n-mz_399.83\t399.833343505859\t5.33034209363829e-10\t0\t1.173826627321e-09\t220.216002406666\t4.79730788427446e-09\t2\n-mz_399.92\t399.916687011719\t3.73221996517891e-10\t0\t8.39290456755431e-10\t224.877007407359\t3.35899796866101e-09\t2\n+mz_399.833343505859\t399.833343505859\t5.33034209363829e-10\t0\t1.173826627321e-09\t220.216002406666\t4.79730788427446e-09\t2\n+mz_399.916687011719\t399.916687011719\t3.73221996517891e-10\t0\t8.39290456755431e-10\t224.877007407359\t3.35899796866101e-09\t2\n'
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/features_out3.tabular
--- a/test-data/features_out3.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/features_out3.tabular Thu Apr 23 08:09:32 2020 -0400
b
b'@@ -1,1200 +1,1200 @@\n mz_names\tmz\tsample_mean\tsample_median\tsample_sd\tsample_sem\tintensity_sum\tnumber_peaks\n-mz_300.08\t300.083343505859\t0.0292992062038845\t0\t0.0878976186116536\t300\t0.263692855834961\t1\n-mz_300.17\t300.166687011719\t0.00287774681217141\t0\t0.00863324043651422\t300\t0.0258997213095427\t1\n+mz_300.083343505859\t300.083343505859\t0.0292992062038845\t0\t0.0878976186116536\t300\t0.263692855834961\t1\n+mz_300.166687011719\t300.166687011719\t0.00287774681217141\t0\t0.00863324043651422\t300\t0.0258997213095427\t1\n mz_300.25\t300.25\t1.77280128848483e-10\t0\t5.31840386545449e-10\t300\t1.59552115963635e-09\t1\n-mz_300.33\t300.333343505859\t5.14883475361611e-11\t0\t1.54465042608483e-10\t300\t4.6339512782545e-10\t1\n-mz_300.42\t300.416687011719\t4.0139211399115e-12\t0\t1.20417634197345e-11\t300\t3.61252902592035e-11\t1\n+mz_300.333343505859\t300.333343505859\t5.14883475361611e-11\t0\t1.54465042608483e-10\t300\t4.6339512782545e-10\t1\n+mz_300.416687011719\t300.416687011719\t4.0139211399115e-12\t0\t1.20417634197345e-11\t300\t3.61252902592035e-11\t1\n mz_300.5\t300.5\t5.50704215937811e-06\t0\t1.65211264781343e-05\t300\t4.9563379434403e-05\t1\n-mz_300.58\t300.583343505859\t3.95111985401147e-06\t0\t1.18533595620344e-05\t300\t3.55600786861032e-05\t1\n-mz_300.67\t300.666687011719\t7.27397238935939e-07\t0\t2.18219171680782e-06\t300\t6.54657515042345e-06\t1\n+mz_300.583343505859\t300.583343505859\t3.95111985401147e-06\t0\t1.18533595620344e-05\t300\t3.55600786861032e-05\t1\n+mz_300.666687011719\t300.666687011719\t7.27397238935939e-07\t0\t2.18219171680782e-06\t300\t6.54657515042345e-06\t1\n mz_300.75\t300.75\t1.30250899042089e-14\t0\t3.90752697126268e-14\t300\t1.1722580913788e-13\t1\n-mz_300.83\t300.833343505859\t7.27670494871757e-15\t0\t2.18301148461527e-14\t300\t6.54903445384582e-14\t1\n-mz_300.92\t300.916687011719\t1.19033973005598e-15\t0\t3.57101919016793e-15\t300\t1.07130575705038e-14\t1\n+mz_300.833343505859\t300.833343505859\t7.27670494871757e-15\t0\t2.18301148461527e-14\t300\t6.54903445384582e-14\t1\n+mz_300.916687011719\t300.916687011719\t1.19033973005598e-15\t0\t3.57101919016793e-15\t300\t1.07130575705038e-14\t1\n mz_301\t301\t0\t0\t0\tNA\t0\t0\n-mz_301.08\t301.083343505859\t4.24474381569932e-10\t0\t1.2734231447098e-09\t300\t3.82026943412939e-09\t1\n-mz_301.17\t301.166687011719\t1.2672437173696e-10\t0\t3.8017311521088e-10\t300\t1.14051934563264e-09\t1\n+mz_301.083343505859\t301.083343505859\t4.24474381569932e-10\t0\t1.2734231447098e-09\t300\t3.82026943412939e-09\t1\n+mz_301.166687011719\t301.166687011719\t1.2672437173696e-10\t0\t3.8017311521088e-10\t300\t1.14051934563264e-09\t1\n mz_301.25\t301.25\t1.04927193477088e-11\t0\t3.14781580431263e-11\t300\t9.4434474129379e-11\t1\n-mz_301.33\t301.333343505859\t8.29418595654768e-19\t0\t2.4882557869643e-18\t300\t7.46476736089292e-18\t1\n-mz_301.42\t301.416687011719\t2.20798332887492e-19\t0\t6.62394998662477e-19\t300\t1.98718499598743e-18\t1\n+mz_301.333343505859\t301.333343505859\t8.29418595654768e-19\t0\t2.4882557869643e-18\t300\t7.46476736089292e-18\t1\n+mz_301.416687011719\t301.416687011719\t2.20798332887492e-19\t0\t6.62394998662477e-19\t300\t1.98718499598743e-18\t1\n mz_301.5\t301.5\t1.36295095239794e-20\t0\t4.08885285719383e-20\t300\t1.22665585715815e-19\t1\n-mz_301.58\t301.583343505859\t3.00898357879359e-14\t0\t9.02695073638077e-14\t300\t2.70808522091423e-13\t1\n-mz_301.67\t301.666687011719\t1.77132674365446e-14\t0\t5.31398023096337e-14\t300\t1.59419406928901e-13\t1\n+mz_301.583343505859\t301.583343505859\t3.00898357879359e-14\t0\t9.02695073638077e-14\t300\t2.70808522091423e-13\t1\n+mz_301.666687011719\t301.666687011719\t1.77132674365446e-14\t0\t5.31398023096337e-14\t300\t1.59419406928901e-13\t1\n mz_301.75\t301.75\t2.98124144276739e-15\t0\t8.94372432830217e-15\t300\t2.68311729849065e-14\t1\n-mz_301.83\t301.833343505859\t6.7355936850742e-23\t0\t2.02067810552226e-22\t300\t6.06203431656678e-22\t1\n-mz_301.92\t301.916687011719\t3.23492041045198e-23\t0\t9.70476123135593e-23\t300\t2.91142836940678e-22\t1\n+mz_301.833343505859\t301.833343505859\t6.7355936850742e-23\t0\t2.02067810552226e-22\t300\t6.06203431656678e-22\t1\n+mz_301.916687011719\t301.916687011719\t3.23492041045198e-23\t0\t9.70476123135593e-23\t300\t2.91142836940678e-22\t1\n mz_302\t302\t4.80219917504923e-24\t0\t1.440659752'..b'87e-07\t300\t4.5503847445616e-07\t2\n-mz_397.92\t397.916687011719\t2.1973092932285e-23\t0\t6.59192787967557e-23\t299.999999999548\t1.97757836390565e-22\t2\n+mz_397.833343505859\t397.833343505859\t5.05598304951289e-08\t0\t1.51679491485387e-07\t300\t4.5503847445616e-07\t2\n+mz_397.916687011719\t397.916687011719\t2.1973092932285e-23\t0\t6.59192787967557e-23\t299.999999999548\t1.97757836390565e-22\t2\n mz_398\t398\t3.04395583748723e-24\t0\t9.13186751242318e-24\t299.999999998735\t2.73956025373851e-23\t2\n-mz_398.08\t398.083343505859\t0.00435541777147187\t0\t0.0130662533144156\t300\t0.0391987599432468\t3\n-mz_398.17\t398.166687011719\t0.0476158229749465\t0\t0.142847468396982\t299.999998891423\t0.428542406774519\t3\n+mz_398.083343505859\t398.083343505859\t0.00435541777147187\t0\t0.0130662533144156\t300\t0.0391987599432468\t3\n+mz_398.166687011719\t398.166687011719\t0.0476158229749465\t0\t0.142847468396982\t299.999998891423\t0.428542406774519\t3\n mz_398.25\t398.25\t0.0337751011944952\t0\t0.101325303282695\t299.999999109431\t0.303975910750457\t3\n-mz_398.33\t398.333343505859\t0.00567932097266618\t0\t0.017037962868249\t299.999999124024\t0.0511138887539956\t2\n-mz_398.42\t398.416687011719\t0\t0\t0\tNA\t0\t0\n+mz_398.333343505859\t398.333343505859\t0.00567932097266618\t0\t0.017037962868249\t299.999999124024\t0.0511138887539956\t2\n+mz_398.416687011719\t398.416687011719\t0\t0\t0\tNA\t0\t0\n mz_398.5\t398.5\t1.45001195853997e-39\t0\t4.35003587561991e-39\t300\t1.30501076268597e-38\t1\n-mz_398.58\t398.583343505859\t5.86734578455249e-32\t0\t1.76020373536575e-31\t300\t5.28061120609724e-31\t1\n-mz_398.67\t398.666687011719\t0.00365118661688434\t0\t0.0075229081301236\t206.040088319099\t0.032860679551959\t3\n+mz_398.583343505859\t398.583343505859\t5.86734578455249e-32\t0\t1.76020373536575e-31\t300\t5.28061120609724e-31\t1\n+mz_398.666687011719\t398.666687011719\t0.00365118661688434\t0\t0.0075229081301236\t206.040088319099\t0.032860679551959\t3\n mz_398.75\t398.75\t0.0974471403492822\t0\t0.218609809238247\t224.336813224769\t0.877024263143539\t3\n-mz_398.83\t398.833343505859\t0.0827518999576569\t0\t0.185963341513219\t224.723953901208\t0.744767099618912\t3\n-mz_398.92\t398.916687011719\t0.0164484298891491\t0\t0.037280611765694\t226.651492069086\t0.148035869002342\t2\n+mz_398.833343505859\t398.833343505859\t0.0827518999576569\t0\t0.185963341513219\t224.723953901208\t0.744767099618912\t3\n+mz_398.916687011719\t398.916687011719\t0.0164484298891491\t0\t0.037280611765694\t226.651492069086\t0.148035869002342\t2\n mz_399\t399\t0\t0\t0\tNA\t0\t0\n-mz_399.08\t399.083343505859\t0\t0\t0\tNA\t0\t0\n-mz_399.17\t399.166687011719\t2.12591405853366e-35\t0\t6.37774217560099e-35\t300\t1.9133226526803e-34\t1\n+mz_399.083343505859\t399.083343505859\t0\t0\t0\tNA\t0\t0\n+mz_399.166687011719\t399.166687011719\t2.12591405853366e-35\t0\t6.37774217560099e-35\t300\t1.9133226526803e-34\t1\n mz_399.25\t399.25\t8.92074257340149e-36\t0\t2.67622277202045e-35\t300\t8.02866831606135e-35\t1\n-mz_399.33\t399.333343505859\t8.50251995466857e-06\t0\t1.90083935605297e-05\t223.561881205496\t7.65226795920171e-05\t3\n-mz_399.42\t399.416687011719\t2.75656642164298e-06\t0\t6.22119222208426e-06\t225.686280339158\t2.48090977947868e-05\t2\n+mz_399.333343505859\t399.333343505859\t8.50251995466857e-06\t0\t1.90083935605297e-05\t223.561881205496\t7.65226795920171e-05\t3\n+mz_399.416687011719\t399.416687011719\t2.75656642164298e-06\t0\t6.22119222208426e-06\t225.686280339158\t2.48090977947868e-05\t2\n mz_399.5\t399.5\t2.66098109275643e-07\t0\t6.10309301715427e-07\t229.354993681382\t2.39488298348078e-06\t2\n-mz_399.58\t399.583343505859\t0\t0\t0\tNA\t0\t0\n-mz_399.67\t399.666687011719\t0\t0\t0\tNA\t0\t0\n+mz_399.583343505859\t399.583343505859\t0\t0\t0\tNA\t0\t0\n+mz_399.666687011719\t399.666687011719\t0\t0\t0\tNA\t0\t0\n mz_399.75\t399.75\t0\t0\t0\tNA\t0\t0\n-mz_399.83\t399.833343505859\t5.33034209363829e-10\t0\t1.173826627321e-09\t220.216002406666\t4.79730788427446e-09\t2\n-mz_399.92\t399.916687011719\t3.73221996517891e-10\t0\t8.39290456755431e-10\t224.877007407359\t3.35899796866101e-09\t2\n+mz_399.833343505859\t399.833343505859\t5.33034209363829e-10\t0\t1.173826627321e-09\t220.216002406666\t4.79730788427446e-09\t2\n+mz_399.916687011719\t399.916687011719\t3.73221996517891e-10\t0\t8.39290456755431e-10\t224.877007407359\t3.35899796866101e-09\t2\n'
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/features_out4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out4.tabular Thu Apr 23 08:09:32 2020 -0400
b
b'@@ -0,0 +1,10399 @@\n+mz_names\tmz\tsample_mean\tsample_median\tsample_sd\tsample_sem\tintensity_sum\tnumber_peaks\n+mz_100\t100\t0\t0\t0\tNA\t0\t0\n+mz_100.0200020002\t100.0200020002\t0\t0\t0\tNA\t0\t0\n+mz_100.0400080012\t100.0400080012\t0\t0\t0\tNA\t0\t0\n+mz_100.060018003801\t100.060018003801\t0\t0\t0\tNA\t0\t0\n+mz_100.080032008802\t100.080032008802\t0\t0\t0\tNA\t0\t0\n+mz_100.100050017005\t100.100050017005\t0\t0\t0\tNA\t0\t0\n+mz_100.120072029209\t100.120072029209\t0\t0\t0\tNA\t0\t0\n+mz_100.140098046217\t100.140098046217\t0\t0\t0\tNA\t0\t0\n+mz_100.160128068828\t100.160128068828\t0\t0\t0\tNA\t0\t0\n+mz_100.180162097845\t100.180162097845\t0\t0\t0\tNA\t0\t0\n+mz_100.200200134068\t100.200200134068\t0\t0\t0\tNA\t0\t0\n+mz_100.220242178299\t100.220242178299\t0\t0\t0\tNA\t0\t0\n+mz_100.24028823134\t100.24028823134\t0\t0\t0\tNA\t0\t0\n+mz_100.260338293993\t100.260338293993\t0\t0\t0\tNA\t0\t0\n+mz_100.280392367059\t100.280392367059\t0\t0\t0\tNA\t0\t0\n+mz_100.300450451341\t100.300450451341\t0\t0\t0\tNA\t0\t0\n+mz_100.320512547641\t100.320512547641\t0\t0\t0\tNA\t0\t0\n+mz_100.340578656761\t100.340578656761\t0\t0\t0\tNA\t0\t0\n+mz_100.360648779505\t100.360648779505\t0\t0\t0\tNA\t0\t0\n+mz_100.380722916674\t100.380722916674\t0\t0\t0\tNA\t0\t0\n+mz_100.400801069073\t100.400801069073\t0\t0\t0\tNA\t0\t0\n+mz_100.420883237504\t100.420883237504\t0\t0\t0\tNA\t0\t0\n+mz_100.44096942277\t100.44096942277\t0\t0\t0\tNA\t0\t0\n+mz_100.461059625675\t100.461059625675\t0\t0\t0\tNA\t0\t0\n+mz_100.481153847022\t100.481153847022\t0\t0\t0\tNA\t0\t0\n+mz_100.501252087615\t100.501252087615\t0\t0\t0\tNA\t0\t0\n+mz_100.521354348259\t100.521354348259\t0\t0\t0\tNA\t0\t0\n+mz_100.541460629757\t100.541460629757\t0\t0\t0\tNA\t0\t0\n+mz_100.561570932913\t100.561570932913\t0\t0\t0\tNA\t0\t0\n+mz_100.581685258532\t100.581685258532\t0.00161491779403554\t0\t0.00484475338210662\t300\t0.0145342601463199\t1\n+mz_100.601803607419\t100.601803607419\t0\t0\t0\tNA\t0\t0\n+mz_100.621925980377\t100.621925980377\t0\t0\t0\tNA\t0\t0\n+mz_100.642052378213\t100.642052378213\t0\t0\t0\tNA\t0\t0\n+mz_100.662182801731\t100.662182801731\t0.0295970870388879\t0\t0.0887912611166636\t300\t0.266373783349991\t1\n+mz_100.682317251737\t100.682317251737\t0\t0\t0\tNA\t0\t0\n+mz_100.702455729035\t100.702455729035\t0\t0\t0\tNA\t0\t0\n+mz_100.722598234431\t100.722598234431\t0\t0\t0\tNA\t0\t0\n+mz_100.742744768731\t100.742744768731\t0.027905543645223\t0\t0.0837166309356689\t300\t0.251149892807007\t1\n+mz_100.762895332742\t100.762895332742\t0\t0\t0\tNA\t0\t0\n+mz_100.783049927268\t100.783049927268\t0\t0\t0\tNA\t0\t0\n+mz_100.803208553116\t100.803208553116\t0\t0\t0\tNA\t0\t0\n+mz_100.823371211092\t100.823371211092\t0.0083441242782606\t0\t0.0201507346585991\t241.496099370175\t0.0750971185043454\t2\n+mz_100.843537902003\t100.843537902003\t0\t0\t0\tNA\t0\t0\n+mz_100.863708626656\t100.863708626656\t0\t0\t0\tNA\t0\t0\n+mz_100.883883385858\t100.883883385858\t0\t0\t0\tNA\t0\t0\n+mz_100.904062180414\t100.904062180414\t0\t0\t0\tNA\t0\t0\n+mz_100.924245011133\t100.924245011133\t0.0367837401055214\t0\t0.0819494717398366\t222.787219311436\t0.331053660949692\t3\n+mz_100.944431878822\t100.944431878822\t0\t0\t0\tNA\t0\t0\n+mz_100.964622784289\t100.964622784289\t0\t0\t0\tNA\t0\t0\n+mz_100.98481772834\t100.98481772834\t0\t0\t0\tNA\t0\t0\n+mz_101.005016711784\t101.005016711784\t0.062111565636264\t0\t0.118073778962174\t190.099505225217\t0.559004090726376\t3\n+mz_101.025219735429\t101.025219735429\t0\t0\t0\tNA\t0\t0\n+mz_101.045426800082\t101.045426800082\t0\t0\t0\tNA\t0\t0\n+mz_101.065637906553\t101.065637906553\t0\t0\t0\tNA\t0\t0\n+mz_101.085853055649\t101.085853055649\t0.125321019026968\t0\t0.229086966323655\t182.800114539731\t1.12788917124271\t3\n+mz_101.106072248179\t101.106072248179\t0\t0\t0\tNA\t0\t0\n+mz_101.126295484953\t101.126295484953\t0\t0\t0\tNA\t0\t0\n+mz_101.146522766778\t101.146522766778\t0\t0\t0\tNA\t0\t0\n+mz_101.166754094464\t101.166754094464\t0.110433474390043\t0\t0.241764556418413\t218.923254704925\t0.993901269510388\t3\n+mz_101.18698946882\t101.18698946882\t0\t0\t0\tNA\t0\t0\n+mz_101.207228890656\t101.207228890656\t0\t0\t0\tNA\t0\t0\n+mz_101.227472360782\t101.227472360782\t0\t0\t0\tNA\t0\t0\n+mz_101.247719880006\t101.247719880006\t0.0220825859572263\t0\t0.0489671939640457\t221.745741458426\t0.198743273615037\t3\n+mz_101.267971449139\t101.267971449139\t0\t0\t0\tNA\t0\t0\n+mz_101.28822706899\t101.28822706899\t0\t0\t0\tNA\t0\t0\n+mz_101.308486740371\t101.308486740371\t0\t0\t0\tNA\t0\t0\n+mz_101.328750464092\t101.328750464092'..b'\t0.109568835592831\t292.414989166609\t0.337232890538871\t2\n+mz_794.704377181409\t794.704377181409\t0.15831301940812\t1.39839147066058e-38\t0.342155960501196\t216.126230034904\t1.42481717467308\t5\n+mz_794.863333952522\t794.863333952522\t0.061700455553364\t2.09150662162954e-38\t0.147614505083265\t239.243784765243\t0.555304099980276\t6\n+mz_795.022322518169\t795.022322518169\t0.0108078516398867\t0\t0.0324235549196601\t300\t0.0972706647589803\t1\n+mz_79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b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/features_test6.tabular
--- a/test-data/features_test6.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/features_test6.tabular Thu Apr 23 08:09:32 2020 -0400
b
b'@@ -1,9 +1,25 @@\n mz\tr\tk\ts\tclasses\tcenters\ttstatistics\tp.values\tadj.p.values\n-928.859680175781\t2\t3\t2\tB\t43.951696\t0.541815\t0.607464\t1\n-912.877136230469\t2\t3\t2\tB\t55.419364\t0.437808\t0.676846\t1\n-913.887756347656\t2\t3\t2\tB\t24.914021\t0.39334\t0.707664\t1\n-930.862670898438\t2\t3\t2\tB\t9.285831\t0.298582\t0.77533\t1\n-913.923889160156\t2\t3\t2\tB\t12.149184\t0.096006\t0.926642\t1\n+928.859680175781\t2\t3\t2\tB\t46.866973\t1.152552\t0.313286\t1\n+912.877136230469\t2\t3\t2\tB\t58.999545\t0.929502\t0.405243\t1\n+913.887756347656\t2\t3\t2\tB\t26.415843\t0.909835\t0.414375\t1\n+930.862670898438\t2\t3\t2\tB\t9.993604\t0.863196\t0.436714\t1\n+913.923889160156\t2\t3\t2\tB\t12.760526\t0.476861\t0.658344\t1\n+900.3271484375\t2\t3\t2\tA\t6.121557\t0.376277\t0.722149\t1\n+913.743347167969\t2\t3\t2\tB\t3.417349\t0.264134\t0.804727\t1\n+913.165832519531\t2\t3\t2\tB\t3.829102\t0.194428\t0.855316\t1\n+931.846740722656\t2\t3\t2\tB\t4.546124\t0.193106\t0.856285\t1\n+929.879089355469\t2\t3\t2\tB\t16.314458\t0.190147\t0.858454\t1\n+937.10400390625\t2\t3\t2\tB\t3.028836\t0.16665\t0.87573\t1\n+944.834045410156\t2\t3\t2\tB\t11.957613\t0.164794\t0.877099\t1\n+917.103881835938\t2\t3\t2\tB\t9.707931\t0.126322\t0.905572\t1\n+955.805419921875\t2\t3\t2\tB\t2.960784\t0.111464\t0.916618\t1\n+922.355712890625\t2\t3\t2\tA\t6.269198\t0.09738\t0.926208\t1\n+913.021484375\t2\t3\t2\tB\t6.344582\t0.082951\t0.937876\t1\n+907.508483886719\t2\t3\t2\tA\t6.358292\t0.081166\t0.938459\t1\n+912.768920898438\t2\t3\t2\tB\t4.709596\t0.063477\t0.952432\t1\n+943.989868164062\t2\t3\t2\tB\t2.730518\t0.038768\t0.970933\t1\n+933.451599121094\t2\t3\t2\tA\t3.775416\t0.027483\t0.979138\t1\n+914.862854003906\t2\t3\t2\tB\t7.511109\t0.007433\t0.994425\t1\n 900.004699707031\t2\t3\t2\tA\t2.291667\t0\t1\t1\n 900.04052734375\t2\t3\t2\tA\t3.125\t0\t1\t1\n 900.076354980469\t2\t3\t2\tA\t3.333333\t0\t1\t1\n@@ -13,7 +29,6 @@\n 900.219665527344\t2\t3\t2\tA\t3.666667\t0\t1\t1\n 900.255493164062\t2\t3\t2\tA\t3.916667\t0\t1\t1\n 900.291320800781\t2\t3\t2\tA\t4.083333\t0\t1\t1\n-900.3271484375\t2\t3\t2\tA\t5.791667\t0\t1\t1\n 900.362976074219\t2\t3\t2\tA\t11.541667\t0\t1\t1\n 900.398864746094\t2\t3\t2\tA\t26.208333\t0\t1\t1\n 900.434692382812\t2\t3\t2\tA\t30.041667\t0\t1\t1\n@@ -213,7 +228,6 @@\n 907.400573730469\t2\t3\t2\tA\t30\t0\t1\t1\n 907.4365234375\t2\t3\t2\tA\t13.5\t0\t1\t1\n 907.472534179688\t2\t3\t2\tA\t8.916667\t0\t1\t1\n-907.508483886719\t2\t3\t2\tA\t6.291667\t0\t1\t1\n 907.544494628906\t2\t3\t2\tA\t5.208333\t0\t1\t1\n 907.580444335938\t2\t3\t2\tA\t4.125\t0\t1\t1\n 907.616455078125\t2\t3\t2\tA\t4.041667\t0\t1\t1\n@@ -624,7 +638,6 @@\n 922.246887207031\t2\t3\t2\tA\t3.125\t0\t1\t1\n 922.283142089844\t2\t3\t2\tA\t4.25\t0\t1\t1\n 922.319458007812\t2\t3\t2\tA\t5.208333\t0\t1\t1\n-922.355712890625\t2\t3\t2\tA\t6.166667\t0\t1\t1\n 922.391967773438\t2\t3\t2\tA\t4.916667\t0\t1\t1\n 922.42822265625\t2\t3\t2\tA\t4.666667\t0\t1\t1\n 922.464538574219\t2\t3\t2\tA\t3.375\t0\t1\t1\n@@ -929,7 +942,6 @@\n 933.342102050781\t2\t3\t2\tA\t7.416667\t0\t1\t1\n 933.378601074219\t2\t3\t2\tA\t8.5\t0\t1\t1\n 933.415100097656\t2\t3\t2\tA\t6.416667\t0\t1\t1\n-933.451599121094\t2\t3\t2\tA\t3.75\t0\t1\t1\n 933.488037109375\t2\t3\t2\tA\t3.166667\t0\t1\t1\n 933.524536132812\t2\t3\t2\tA\t2.916667\t0\t1\t1\n 933.56103515625\t2\t3\t2\tA\t2.958333\t0\t1\t1\n@@ -3077,17 +3089,14 @@\n 912.66064453125\t2\t3\t2\tB\t2.708333\t0\t1\t1\n 912.696716308594\t2\t3\t2\tB\t2.708333\t0\t1\t1\n 912.732788085938\t2\t3\t2\tB\t2.75\t0\t1\t1\n-912.768920898438\t2\t3\t2\tB\t4.625\t0\t1\t1\n 912.804992675781\t2\t3\t2\tB\t16.708333\t0\t1\t1\n 912.841064453125\t2\t3\t2\tB\t39.916667\t0\t1\t1\n 912.913208007812\t2\t3\t2\tB\t28.041667\t0\t1\t1\n 912.949340820312\t2\t3\t2\tB\t12\t0\t1\t1\n 912.985412597656\t2\t3\t2\tB\t8.166667\t0\t1\t1\n-913.021484375\t2\t3\t2\tB\t6.25\t0\t1\t1\n 913.057556152344\t2\t3\t2\tB\t5.458333\t0\t1\t1\n 913.093688964844\t2\t3\t2\tB\t4.625\t0\t1\t1\n 913.129760742188\t2\t3\t2\tB\t4.291667\t0\t1\t1\n-913.165832519531\t2\t3\t2\tB\t3.666667\t0\t1\t1\n 913.201904296875\t2\t3\t2\tB\t4.291667\t0\t1\t1\n 913.238037109375\t2\t3\t2\tB\t4.333333\t0\t1\t1\n 913.274108886719\t2\t3\t2\tB\t5\t0\t1\t1\n@@ -3103,7 +3112,6 @@\n 913.635070800781\t2\t3\t2\tB\t3.708333\t0\t1\t1\n 913.671142578125\t2\t3\t2\tB\t3.416667\t0\t1\t1\n 913.707275390625\t2\t3\t2\tB\t3.333333\t0\t1\t1\n-913.743347167969\t2\t3\t2\tB\t3.208333\t0\t1\t1\n 913.779479980469\t2\t3\t2\tB\t4.916667\t0\t1\t1\n 913.815551757812\t2\t3\t2\tB\t11.25\t0\t1\t1\n 913.851684570312\t2\t3\t2\tB\t21.875\t0\t1\t1\n@@ -3132,7 +3140,6 @@\n 914.754516601562\t2\t3\t2\tB\t2.541667\t0\t1\t1\n 914.790588378906\t2\t3\t2\tB\t3.375\t0\t1\t1\n 914.826721191406\t2\t3\t2\tB\t4.875\t0\t1\t1\n-914.862854003906\t2\t3\t2\tB\t7.5\t0\t1\t1\n 914.898986'..b'\t3.208333\t0\t1\t1\n+996.475280761719\t2\t3\t2\tC\t3.333333\t0\t1\t1\n+996.512939453125\t2\t3\t2\tC\t3.041667\t0\t1\t1\n+996.550659179688\t2\t3\t2\tC\t2.666667\t0\t1\t1\n+996.58837890625\t2\t3\t2\tC\t2.5\t0\t1\t1\n+996.626098632812\t2\t3\t2\tC\t2.291667\t0\t1\t1\n+996.663757324219\t2\t3\t2\tC\t2.291667\t0\t1\t1\n+996.701477050781\t2\t3\t2\tC\t1.916667\t0\t1\t1\n+996.739196777344\t2\t3\t2\tC\t1.666667\t0\t1\t1\n+996.776916503906\t2\t3\t2\tC\t2.166667\t0\t1\t1\n+996.814575195312\t2\t3\t2\tC\t1.791667\t0\t1\t1\n+996.852294921875\t2\t3\t2\tC\t1.958333\t0\t1\t1\n+996.890014648438\t2\t3\t2\tC\t2.375\t0\t1\t1\n+996.927734375\t2\t3\t2\tC\t2\t0\t1\t1\n+996.965454101562\t2\t3\t2\tC\t1.875\t0\t1\t1\n+997.003112792969\t2\t3\t2\tC\t2.125\t0\t1\t1\n+997.040832519531\t2\t3\t2\tC\t1.916667\t0\t1\t1\n+997.078552246094\t2\t3\t2\tC\t2.041667\t0\t1\t1\n+997.116271972656\t2\t3\t2\tC\t2.125\t0\t1\t1\n+997.153991699219\t2\t3\t2\tC\t2.208333\t0\t1\t1\n+997.191711425781\t2\t3\t2\tC\t2.5\t0\t1\t1\n+997.229431152344\t2\t3\t2\tC\t2.625\t0\t1\t1\n+997.267150878906\t2\t3\t2\tC\t2.666667\t0\t1\t1\n+997.304870605469\t2\t3\t2\tC\t3.25\t0\t1\t1\n+997.342590332031\t2\t3\t2\tC\t3.041667\t0\t1\t1\n+997.380249023438\t2\t3\t2\tC\t3.25\t0\t1\t1\n+997.41796875\t2\t3\t2\tC\t3.333333\t0\t1\t1\n+997.455688476562\t2\t3\t2\tC\t3.083333\t0\t1\t1\n+997.493408203125\t2\t3\t2\tC\t2.75\t0\t1\t1\n+997.531127929688\t2\t3\t2\tC\t2.5\t0\t1\t1\n+997.56884765625\t2\t3\t2\tC\t2.375\t0\t1\t1\n+997.606567382812\t2\t3\t2\tC\t2.333333\t0\t1\t1\n+997.644348144531\t2\t3\t2\tC\t1.875\t0\t1\t1\n+997.682067871094\t2\t3\t2\tC\t1.666667\t0\t1\t1\n+997.719787597656\t2\t3\t2\tC\t1.875\t0\t1\t1\n+997.757507324219\t2\t3\t2\tC\t2.083333\t0\t1\t1\n+997.795227050781\t2\t3\t2\tC\t1.791667\t0\t1\t1\n+997.832946777344\t2\t3\t2\tC\t1.625\t0\t1\t1\n+997.870666503906\t2\t3\t2\tC\t1.916667\t0\t1\t1\n+997.908386230469\t2\t3\t2\tC\t1.958333\t0\t1\t1\n+997.946105957031\t2\t3\t2\tC\t2.166667\t0\t1\t1\n+997.983825683594\t2\t3\t2\tC\t2.458333\t0\t1\t1\n+998.021606445312\t2\t3\t2\tC\t2\t0\t1\t1\n+998.059326171875\t2\t3\t2\tC\t2\t0\t1\t1\n+998.097045898438\t2\t3\t2\tC\t2.625\t0\t1\t1\n+998.134765625\t2\t3\t2\tC\t2.416667\t0\t1\t1\n+998.172485351562\t2\t3\t2\tC\t2.875\t0\t1\t1\n+998.210266113281\t2\t3\t2\tC\t2.458333\t0\t1\t1\n+998.247985839844\t2\t3\t2\tC\t2.458333\t0\t1\t1\n+998.285705566406\t2\t3\t2\tC\t3.291667\t0\t1\t1\n+998.323425292969\t2\t3\t2\tC\t3.583333\t0\t1\t1\n+998.361206054688\t2\t3\t2\tC\t3.458333\t0\t1\t1\n+998.39892578125\t2\t3\t2\tC\t3.458333\t0\t1\t1\n+998.436645507812\t2\t3\t2\tC\t3.666667\t0\t1\t1\n+998.474365234375\t2\t3\t2\tC\t3\t0\t1\t1\n+998.512145996094\t2\t3\t2\tC\t2.583333\t0\t1\t1\n+998.549865722656\t2\t3\t2\tC\t2.791667\t0\t1\t1\n+998.587585449219\t2\t3\t2\tC\t2.5\t0\t1\t1\n+998.625366210938\t2\t3\t2\tC\t2.541667\t0\t1\t1\n+998.6630859375\t2\t3\t2\tC\t2.125\t0\t1\t1\n+998.700805664062\t2\t3\t2\tC\t2.125\t0\t1\t1\n+998.738586425781\t2\t3\t2\tC\t2.458333\t0\t1\t1\n+998.776306152344\t2\t3\t2\tC\t1.833333\t0\t1\t1\n+998.814086914062\t2\t3\t2\tC\t1.916667\t0\t1\t1\n+998.851806640625\t2\t3\t2\tC\t1.625\t0\t1\t1\n+998.889526367188\t2\t3\t2\tC\t2.041667\t0\t1\t1\n+998.927307128906\t2\t3\t2\tC\t2.25\t0\t1\t1\n+998.965026855469\t2\t3\t2\tC\t2.041667\t0\t1\t1\n+999.002807617188\t2\t3\t2\tC\t1.791667\t0\t1\t1\n+999.04052734375\t2\t3\t2\tC\t1.958333\t0\t1\t1\n+999.078308105469\t2\t3\t2\tC\t2.458333\t0\t1\t1\n+999.116027832031\t2\t3\t2\tC\t2.833333\t0\t1\t1\n+999.15380859375\t2\t3\t2\tC\t2.958333\t0\t1\t1\n+999.191528320312\t2\t3\t2\tC\t2.583333\t0\t1\t1\n+999.229309082031\t2\t3\t2\tC\t2.833333\t0\t1\t1\n+999.267028808594\t2\t3\t2\tC\t3.166667\t0\t1\t1\n+999.304809570312\t2\t3\t2\tC\t3.666667\t0\t1\t1\n+999.342529296875\t2\t3\t2\tC\t3.375\t0\t1\t1\n+999.380310058594\t2\t3\t2\tC\t3.708333\t0\t1\t1\n+999.418090820312\t2\t3\t2\tC\t4.041667\t0\t1\t1\n+999.455810546875\t2\t3\t2\tC\t3.666667\t0\t1\t1\n+999.493591308594\t2\t3\t2\tC\t3.125\t0\t1\t1\n+999.531311035156\t2\t3\t2\tC\t2.625\t0\t1\t1\n+999.569091796875\t2\t3\t2\tC\t2.333333\t0\t1\t1\n+999.606872558594\t2\t3\t2\tC\t2.041667\t0\t1\t1\n+999.644592285156\t2\t3\t2\tC\t2.041667\t0\t1\t1\n+999.682373046875\t2\t3\t2\tC\t2.125\t0\t1\t1\n+999.720153808594\t2\t3\t2\tC\t1.958333\t0\t1\t1\n+999.757873535156\t2\t3\t2\tC\t2.125\t0\t1\t1\n+999.795654296875\t2\t3\t2\tC\t2\t0\t1\t1\n+999.833435058594\t2\t3\t2\tC\t1.875\t0\t1\t1\n+999.871215820312\t2\t3\t2\tC\t2.125\t0\t1\t1\n+999.908935546875\t2\t3\t2\tC\t1.958333\t0\t1\t1\n+999.946716308594\t2\t3\t2\tC\t1.833333\t0\t1\t1\n+999.984497070312\t2\t3\t2\tC\t1.916667\t0\t1\t1\n+928.350158691406\t2\t3\t2\tC\t23.114573\t-0.030053\t0.976518\t1\n+913.310180664062\t2\t3\t2\tC\t4.842616\t-0.134742\t0.89505\t1\n+928.859680175781\t2\t3\t2\tC\t38.383027\t-0.245936\t0.809888\t1\n+910.316955566406\t2\t3\t2\tC\t8.639277\t-0.320083\t0.75441\t1\n+945.825500488281\t2\t3\t2\tC\t6.412327\t-0.331486\t0.745995\t1\n'
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/int_matrix1.tabular
--- a/test-data/int_matrix1.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/int_matrix1.tabular Thu Apr 23 08:09:32 2020 -0400
b
b'@@ -1,1200 +1,1200 @@\n mz_name\txy_1_1\txy_2_1\txy_3_1\txy_1_2\txy_2_2\txy_3_2\txy_1_3\txy_2_3\txy_3_3\n-mz_300.08\t0\t0\t0\t0\t0.263692855834961\t0\t0\t0\t0\n-mz_300.17\t0\t0\t0\t0\t0.0258997213095427\t0\t0\t0\t0\n+mz_300.083343505859\t0\t0\t0\t0\t0.263692855834961\t0\t0\t0\t0\n+mz_300.166687011719\t0\t0\t0\t0\t0.0258997213095427\t0\t0\t0\t0\n mz_300.25\t0\t1.59552115963635e-09\t0\t0\t0\t0\t0\t0\t0\n-mz_300.33\t0\t4.6339512782545e-10\t0\t0\t0\t0\t0\t0\t0\n-mz_300.42\t0\t3.61252902592035e-11\t0\t0\t0\t0\t0\t0\t0\n+mz_300.333343505859\t0\t4.6339512782545e-10\t0\t0\t0\t0\t0\t0\t0\n+mz_300.416687011719\t0\t3.61252902592035e-11\t0\t0\t0\t0\t0\t0\t0\n mz_300.5\t0\t0\t0\t0\t4.9563379434403e-05\t0\t0\t0\t0\n-mz_300.58\t0\t0\t0\t0\t3.55600786861032e-05\t0\t0\t0\t0\n-mz_300.67\t0\t0\t0\t0\t6.54657515042345e-06\t0\t0\t0\t0\n+mz_300.583343505859\t0\t0\t0\t0\t3.55600786861032e-05\t0\t0\t0\t0\n+mz_300.666687011719\t0\t0\t0\t0\t6.54657515042345e-06\t0\t0\t0\t0\n mz_300.75\t0\t1.1722580913788e-13\t0\t0\t0\t0\t0\t0\t0\n-mz_300.83\t0\t6.54903445384582e-14\t0\t0\t0\t0\t0\t0\t0\n-mz_300.92\t0\t1.07130575705038e-14\t0\t0\t0\t0\t0\t0\t0\n+mz_300.833343505859\t0\t6.54903445384582e-14\t0\t0\t0\t0\t0\t0\t0\n+mz_300.916687011719\t0\t1.07130575705038e-14\t0\t0\t0\t0\t0\t0\t0\n mz_301\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-mz_301.08\t0\t0\t0\t0\t3.82026943412939e-09\t0\t0\t0\t0\n-mz_301.17\t0\t0\t0\t0\t1.14051934563264e-09\t0\t0\t0\t0\n+mz_301.083343505859\t0\t0\t0\t0\t3.82026943412939e-09\t0\t0\t0\t0\n+mz_301.166687011719\t0\t0\t0\t0\t1.14051934563264e-09\t0\t0\t0\t0\n mz_301.25\t0\t0\t0\t0\t9.4434474129379e-11\t0\t0\t0\t0\n-mz_301.33\t0\t7.46476736089292e-18\t0\t0\t0\t0\t0\t0\t0\n-mz_301.42\t0\t1.98718499598743e-18\t0\t0\t0\t0\t0\t0\t0\n+mz_301.333343505859\t0\t7.46476736089292e-18\t0\t0\t0\t0\t0\t0\t0\n+mz_301.416687011719\t0\t1.98718499598743e-18\t0\t0\t0\t0\t0\t0\t0\n mz_301.5\t0\t1.22665585715815e-19\t0\t0\t0\t0\t0\t0\t0\n-mz_301.58\t0\t0\t0\t0\t2.70808522091423e-13\t0\t0\t0\t0\n-mz_301.67\t0\t0\t0\t0\t1.59419406928901e-13\t0\t0\t0\t0\n+mz_301.583343505859\t0\t0\t0\t0\t2.70808522091423e-13\t0\t0\t0\t0\n+mz_301.666687011719\t0\t0\t0\t0\t1.59419406928901e-13\t0\t0\t0\t0\n mz_301.75\t0\t0\t0\t0\t2.68311729849065e-14\t0\t0\t0\t0\n-mz_301.83\t0\t6.06203431656678e-22\t0\t0\t0\t0\t0\t0\t0\n-mz_301.92\t0\t2.91142836940678e-22\t0\t0\t0\t0\t0\t0\t0\n+mz_301.833343505859\t0\t6.06203431656678e-22\t0\t0\t0\t0\t0\t0\t0\n+mz_301.916687011719\t0\t2.91142836940678e-22\t0\t0\t0\t0\t0\t0\t0\n mz_302\t0\t4.32197925754431e-23\t0\t0\t0\t0\t0\t0\t0\n-mz_302.08\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-mz_302.17\t0\t0\t0\t0\t1.79306187760221e-17\t0\t0\t0\t0\n+mz_302.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_302.166687011719\t0\t0\t0\t0\t1.79306187760221e-17\t0\t0\t0\t0\n mz_302.25\t0\t0\t0\t0\t4.90061292750663e-18\t0\t0\t0\t0\n-mz_302.33\t0\t7.7875562784001e-27\t0\t0\t3.27269485712631e-19\t0\t0\t0\t0\n-mz_302.42\t0\t3.45923272288949e-26\t0\t0\t0\t0\t0\t0\t0\n+mz_302.333343505859\t0\t7.7875562784001e-27\t0\t0\t3.27269485712631e-19\t0\t0\t0\t0\n+mz_302.416687011719\t0\t3.45923272288949e-26\t0\t0\t0\t0\t0\t0\t0\n mz_302.5\t0\t8.46244064951227e-27\t0\t0\t0\t0\t0\t0\t0\n-mz_302.58\t0\t3.77161794357152e-28\t0\t0\t0\t0\t0\t0\t0\n-mz_302.67\t0\t0\t0\t0.0135595984756947\t1.41553322001893e-21\t0\t0\t0\t0\n+mz_302.583343505859\t0\t3.77161794357152e-28\t0\t0\t0\t0\t0\t0\t0\n+mz_302.666687011719\t0\t0\t0\t0.0135595984756947\t1.41553322001893e-21\t0\t0\t0\t0\n mz_302.75\t0\t0\t0\t0.240113586187363\t7.10063369068687e-22\t0\t0\t0\t0\n-mz_302.83\t0\t0\t0\t0.271635204553604\t1.08665147932087e-22\t0\t0\t0\t0\n-mz_302.92\t0\t3.04753906993054e-30\t0\t0.0669490769505501\t0\t0\t0\t0\t0\n+mz_302.833343505859\t0\t0\t0\t0.271635204553604\t1.08665147932087e-22\t0\t0\t0\t0\n+mz_302.916687011719\t0\t3.04753906993054e-30\t0\t0.0669490769505501\t0\t0\t0\t0\t0\n mz_303\t0\t1.28620729883923e-30\t0\t0.00308917369693518\t0\t0\t0\t0\t0\n-mz_303.08\t0\t1.71799651357141e-31\t0\t0\t0\t0\t0\t0\t0\n-mz_303.17\t0\t0\t0\t0\t8.55154803543523e-27\t0\t0\t0\t0\n+mz_303.083343505859\t0\t1.71799651357141e-31\t0\t0\t0\t0\t0\t0\t0\n+mz_303.166687011719\t0\t0\t0\t0\t8.55154803543523e-27\t0\t0\t0\t0\n mz_303.25\t0\t0\t0\t0\t8.33261879641618e-26\t0\t0\t0\t0\n-mz_303.33\t0\t0\t0\t2.37724270846229e-05\t2.09127303308002e-26\t0\t0\t0\t0\n-mz_303.42\t0\t9.58168691215212e-35\t0\t1.01417299447348e-05\t1.04388012620863e-27\t0\t0\t0\t0\n+mz_303.333343505859\t0\t0\t0\t2.37724270846229e-05\t2.09127303308002e-26\t0\t0\t0\t0\n+mz_303.416687011719\t0\t9.58168691215212e-35\t0\t1.01417299447348e-05\t1.04388012620863e-27\t0\t0\t0\t0\n mz_303.5\t0\t1.58932794058987e-34\t0\t1.36794596983236e-06\t0\t0\t0\t0\t0\n-mz_303.58\t0\t3.57706489580698e-35\t0\t0\t0\t0\t0\t0\t0'..b'11719\t0\t0\t6.85586688738441e-15\t0\t0\t2.28012433765444e-38\t0\t2.33549728191425e-26\t0\n mz_397\t0\t0\t0\t0.0388109683990479\t0\t0\t0\t3.20919536266692e-27\t7.3794850397387e-18\n-mz_397.08\t0\t0\t0\t0.288620352745056\t0\t0\t0\t0\t4.0904726491625e-18\n-mz_397.17\t0\t0\t0\t0.179139345884323\t0\t0\t0\t0\t6.66140851600565e-19\n+mz_397.083343505859\t0\t0\t0\t0.288620352745056\t0\t0\t0\t0\t4.0904726491625e-18\n+mz_397.166687011719\t0\t0\t0\t0.179139345884323\t0\t0\t0\t0\t6.66140851600565e-19\n mz_397.25\t0\t0\t4.74347756244299e-19\t0.0324370078742504\t0\t0\t0\t0\t0\n-mz_397.33\t0\t0\t5.23588866851877e-18\t0\t0\t0\t0\t1.45252028329413e-30\t0\n-mz_397.42\t0\t0\t1.31735450526457e-18\t0\t0\t0\t0\t2.85723650272451e-30\t0\n+mz_397.333343505859\t0\t0\t5.23588866851877e-18\t0\t0\t0\t0\t1.45252028329413e-30\t0\n+mz_397.416687011719\t0\t0\t1.31735450526457e-18\t0\t0\t0\t0\t2.85723650272451e-30\t0\n mz_397.5\t0\t0\t6.64366394090274e-20\t0\t0\t0\t0\t6.57045764736752e-31\t0\n-mz_397.58\t0\t0\t0\t0\t0\t0\t0\t2.04047937094937e-32\t4.67197860272674e-22\n-mz_397.67\t0\t0\t0\t1.94183921848889e-05\t0\t0\t0\t0\t1.23865323750669e-22\n+mz_397.583343505859\t0\t0\t0\t0\t0\t0\t0\t2.04047937094937e-32\t4.67197860272674e-22\n+mz_397.666687011719\t0\t0\t0\t1.94183921848889e-05\t0\t0\t0\t0\t1.23865323750669e-22\n mz_397.75\t0\t0\t0\t5.69980966247385e-06\t0\t0\t0\t0\t7.54736833499504e-24\n-mz_397.83\t0\t0\t4.49627188988339e-22\t4.5503847445616e-07\t0\t0\t0\t0\t0\n-mz_397.92\t0\t0\t1.977578363903e-22\t0\t0\t0\t0\t2.65117092875872e-34\t0\n+mz_397.833343505859\t0\t0\t4.49627188988339e-22\t4.5503847445616e-07\t0\t0\t0\t0\t0\n+mz_397.916687011719\t0\t0\t1.977578363903e-22\t0\t0\t0\t0\t2.65117092875872e-34\t0\n mz_398\t0\t0\t2.73956025372824e-23\t0\t0\t0\t0\t1.02695755303769e-34\t0\n-mz_398.08\t0\t0\t0.0391987599432468\t0\t0\t0\t0\t1.25882128826124e-35\t3.81025795308296e-26\n-mz_398.17\t0\t0\t0.428542405366898\t1.40762135281136e-09\t0\t0\t0\t0\t1.81789914120271e-26\n+mz_398.083343505859\t0\t0\t0.0391987599432468\t0\t0\t0\t0\t1.25882128826124e-35\t3.81025795308296e-26\n+mz_398.166687011719\t0\t0\t0.428542405366898\t1.40762135281136e-09\t0\t0\t0\t0\t1.81789914120271e-26\n mz_398.25\t0\t0\t0.303975909948349\t8.02108046649153e-10\t0\t0\t0\t0\t2.6856332332152e-27\n-mz_398.33\t0\t0\t0.0511138886213303\t1.32665364804829e-10\t0\t0\t0\t0\t0\n-mz_398.42\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_398.333343505859\t0\t0\t0.0511138886213303\t1.32665364804829e-10\t0\t0\t0\t0\t0\n+mz_398.416687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n mz_398.5\t0\t0\t0\t0\t0\t0\t0\t1.30501076268597e-38\t0\n-mz_398.58\t0\t0\t0\t0\t0\t0\t0\t0\t5.28061120609724e-31\n-mz_398.67\t0\t0\t0.0123793203383684\t0.0204813592135906\t0\t0\t0\t0\t2.16410654088079e-30\n+mz_398.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t5.28061120609724e-31\n+mz_398.666687011719\t0\t0\t0.0123793203383684\t0.0204813592135906\t0\t0\t0\t0\t2.16410654088079e-30\n mz_398.75\t0\t0\t0.234551697969437\t0.642472565174103\t0\t0\t0\t0\t5.27295168490728e-31\n-mz_398.83\t0\t0\t0.197811514139175\t0.546955585479736\t0\t0\t0\t0\t2.30524654303423e-32\n-mz_398.92\t0\t0\t0.0379873886704445\t0.110048480331898\t0\t0\t0\t0\t0\n+mz_398.833343505859\t0\t0\t0.197811514139175\t0.546955585479736\t0\t0\t0\t0\t2.30524654303423e-32\n+mz_398.916687011719\t0\t0\t0.0379873886704445\t0.110048480331898\t0\t0\t0\t0\t0\n mz_399\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-mz_399.08\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-mz_399.17\t0\t0\t0\t0\t0\t0\t0\t0\t1.9133226526803e-34\n+mz_399.083343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_399.166687011719\t0\t0\t0\t0\t0\t0\t0\t0\t1.9133226526803e-34\n mz_399.25\t0\t0\t0\t0\t0\t0\t0\t0\t8.02866831606135e-35\n-mz_399.33\t0\t0\t2.07495213544462e-05\t5.57731582375709e-05\t0\t0\t0\t0\t1.06668980736874e-35\n-mz_399.42\t0\t0\t6.47714978185832e-06\t1.83319480129285e-05\t0\t0\t0\t0\t0\n+mz_399.333343505859\t0\t0\t2.07495213544462e-05\t5.57731582375709e-05\t0\t0\t0\t0\t1.06668980736874e-35\n+mz_399.416687011719\t0\t0\t6.47714978185832e-06\t1.83319480129285e-05\t0\t0\t0\t0\t0\n mz_399.5\t0\t0\t5.85329928526335e-07\t1.80955305495445e-06\t0\t0\t0\t0\t0\n-mz_399.58\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-mz_399.67\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_399.583343505859\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+mz_399.666687011719\t0\t0\t0\t0\t0\t0\t0\t0\t0\n mz_399.75\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-mz_399.83\t0\t0\t1.3805676601919e-09\t3.41674022408256e-09\t0\t0\t0\t0\t0\n-mz_399.92\t0\t0\t8.89724960373428e-10\t2.46927300828759e-09\t0\t0\t0\t0\t0\n+mz_399.833343505859\t0\t0\t1.3805676601919e-09\t3.41674022408256e-09\t0\t0\t0\t0\t0\n+mz_399.916687011719\t0\t0\t8.89724960373428e-10\t2.46927300828759e-09\t0\t0\t0\t0\t0\n'
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/int_matrix3.tabular
--- a/test-data/int_matrix3.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/int_matrix3.tabular Thu Apr 23 08:09:32 2020 -0400
b
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diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/kmeans_analyze.pdf
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Binary file test-data/kmeans_analyze.pdf has changed
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diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/mean_out2.tabular
--- a/test-data/mean_out2.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/mean_out2.tabular Thu Apr 23 08:09:32 2020 -0400
b
b'@@ -1,3673 +1,3673 @@\n mz_name\tcol1\tcol2\tcol3\n-mz_1199.47\t30\t10.6666666666667\t21.6666666666667\n-mz_1199.51\t40\t13.6666666666667\t30.6666666666667\n-mz_1199.56\t49.3333333333333\t12.3333333333333\t39.3333333333333\n-mz_1199.6\t48\t14.3333333333333\t37.6666666666667\n-mz_1199.64\t39\t11\t32.3333333333333\n-mz_1199.68\t28.3333333333333\t10.6666666666667\t29.6666666666667\n-mz_1199.72\t22.3333333333333\t10\t18.6666666666667\n-mz_1199.76\t20.3333333333333\t9.33333333333333\t16.3333333333333\n-mz_1199.8\t17.3333333333333\t8.33333333333333\t15.3333333333333\n-mz_1199.85\t15.6666666666667\t7\t13\n-mz_1199.89\t13\t8.66666666666667\t12\n-mz_1199.93\t10.3333333333333\t8.66666666666667\t10\n-mz_1199.97\t11.6666666666667\t8.66666666666667\t9.33333333333333\n-mz_1200.01\t11.6666666666667\t8.33333333333333\t9.33333333333333\n-mz_1200.05\t10.6666666666667\t6.33333333333333\t7.66666666666667\n-mz_1200.09\t13\t9.33333333333333\t9.66666666666667\n-mz_1200.14\t11.6666666666667\t8\t9.33333333333333\n-mz_1200.18\t9.33333333333333\t9\t8.66666666666667\n-mz_1200.22\t10.3333333333333\t7.66666666666667\t9.33333333333333\n-mz_1200.26\t10.6666666666667\t6.66666666666667\t9.66666666666667\n-mz_1200.3\t10.3333333333333\t6.66666666666667\t10\n-mz_1200.34\t13.3333333333333\t9.66666666666667\t14.3333333333333\n-mz_1200.38\t16.3333333333333\t9.33333333333333\t12\n-mz_1200.42\t15.3333333333333\t9\t14.3333333333333\n-mz_1200.47\t19\t9\t15.6666666666667\n-mz_1200.51\t24.3333333333333\t11.3333333333333\t22.3333333333333\n-mz_1200.55\t29\t10.6666666666667\t21.6666666666667\n-mz_1200.59\t28.3333333333333\t11\t22.3333333333333\n-mz_1200.63\t25\t9.33333333333333\t18\n-mz_1200.67\t19.6666666666667\t8.66666666666667\t17.3333333333333\n-mz_1200.71\t17.6666666666667\t7.66666666666667\t12.3333333333333\n-mz_1200.76\t14.3333333333333\t8.33333333333333\t12\n-mz_1200.8\t14\t7.33333333333333\t10.6666666666667\n-mz_1200.84\t11.3333333333333\t7.66666666666667\t11\n-mz_1200.88\t11.3333333333333\t8.33333333333333\t10.3333333333333\n-mz_1200.92\t9\t8.66666666666667\t10.3333333333333\n-mz_1200.96\t11\t7\t8.66666666666667\n-mz_1201\t10.3333333333333\t9\t9.66666666666667\n-mz_1201.05\t10\t7.66666666666667\t9.33333333333333\n-mz_1201.09\t9.33333333333333\t8.33333333333333\t9.33333333333333\n-mz_1201.13\t11\t7.66666666666667\t9\n-mz_1201.17\t10\t8.33333333333333\t9\n-mz_1201.21\t10.3333333333333\t8.66666666666667\t10.3333333333333\n-mz_1201.25\t11.3333333333333\t7.33333333333333\t9\n-mz_1201.29\t12.3333333333333\t8.33333333333333\t9\n-mz_1201.33\t13.3333333333333\t10\t12\n-mz_1201.38\t19.3333333333333\t9\t11\n-mz_1201.42\t21.6666666666667\t9.66666666666667\t16.3333333333333\n-mz_1201.46\t20.6666666666667\t11\t17.3333333333333\n-mz_1201.5\t20.3333333333333\t9.66666666666667\t16\n-mz_1201.54\t21\t9.66666666666667\t18\n-mz_1201.58\t19.6666666666667\t9.33333333333333\t18\n-mz_1201.62\t15.6666666666667\t8.33333333333333\t12\n-mz_1201.67\t15\t7.33333333333333\t11.3333333333333\n-mz_1201.71\t14\t9\t11.6666666666667\n-mz_1201.75\t11.6666666666667\t7\t11.3333333333333\n-mz_1201.79\t13.3333333333333\t8\t10\n-mz_1201.83\t10\t7\t9.66666666666667\n-mz_1201.87\t11.6666666666667\t7\t9\n-mz_1201.91\t9.33333333333333\t7.66666666666667\t8.33333333333333\n-mz_1201.96\t11\t7.66666666666667\t9.66666666666667\n-mz_1202\t9\t7\t9.33333333333333\n-mz_1202.04\t10.3333333333333\t7\t8\n-mz_1202.08\t9.66666666666667\t8\t7.66666666666667\n-mz_1202.12\t9.33333333333333\t7.33333333333333\t7.66666666666667\n-mz_1202.16\t10\t8\t10\n-mz_1202.2\t11\t8\t9.33333333333333\n-mz_1202.25\t11.3333333333333\t8.33333333333333\t10\n-mz_1202.29\t13\t7.33333333333333\t8\n-mz_1202.33\t13\t8.33333333333333\t11\n-mz_1202.37\t14.6666666666667\t9.66666666666667\t12\n-mz_1202.41\t15.3333333333333\t8.33333333333333\t11.3333333333333\n-mz_1202.45\t18.3333333333333\t10\t11\n-mz_1202.49\t15.6666666666667\t9.33333333333333\t13.6666666666667\n-mz_1202.54\t16\t8\t14.3333333333333\n-mz_1202.58\t14.3333333333333\t8\t13.6666666666667\n-mz_1202.62\t14\t8\t13\n-mz_1202.66\t11.3333333333333\t8.33333333333333\t11.6666666666667\n-mz_1202.7\t10.3333333333333\t7.33333333333333\t9.66666666666667\n-mz_1202.74\t11\t9\t9.66666666666667\n-mz_1202.78\t12.3333333333333\t7.66666666666667\t8.66666666666667\n-mz_1202.83\t10.3333333333333\t7.66666666666667\t9.66666666666667\n-mz_120'..b'6666666666667\n+mz_1353.00183105469\t9.66666666666667\t7.66666666666667\t8.66666666666667\n+mz_1353.04577636719\t8.66666666666667\t7.33333333333333\t8.33333333333333\n+mz_1353.08972167969\t8.33333333333333\t7.33333333333333\t9.66666666666667\n+mz_1353.13366699219\t10.3333333333333\t9\t8\n+mz_1353.17749023438\t9.66666666666667\t8.33333333333333\t7.66666666666667\n+mz_1353.22143554688\t10.6666666666667\t7.66666666666667\t9\n+mz_1353.26538085938\t8.66666666666667\t7.66666666666667\t9.66666666666667\n+mz_1353.30932617188\t10.3333333333333\t8.33333333333333\t9\n+mz_1353.35327148438\t11\t8\t7.66666666666667\n+mz_1353.39709472656\t13.3333333333333\t8.33333333333333\t9\n+mz_1353.44104003906\t14\t10.6666666666667\t11\n+mz_1353.48498535156\t16\t9.66666666666667\t10.6666666666667\n+mz_1353.52893066406\t16.3333333333333\t10.6666666666667\t13.3333333333333\n+mz_1353.57287597656\t15\t11.6666666666667\t11.6666666666667\n+mz_1353.61682128906\t12.3333333333333\t8.66666666666667\t12.3333333333333\n+mz_1353.66076660156\t11.6666666666667\t10.3333333333333\t12\n+mz_1353.70458984375\t12.3333333333333\t9.33333333333333\t11.3333333333333\n+mz_1353.74853515625\t13.6666666666667\t7.66666666666667\t10.3333333333333\n+mz_1353.79248046875\t11\t8.66666666666667\t9.33333333333333\n+mz_1353.83642578125\t11\t7.33333333333333\t10\n+mz_1353.88037109375\t10\t7.33333333333333\t8.66666666666667\n+mz_1353.92431640625\t9.66666666666667\t6.66666666666667\t8\n+mz_1353.96826171875\t10\t8.66666666666667\t9.33333333333333\n+mz_1354.01220703125\t9.33333333333333\t8.66666666666667\t9.33333333333333\n+mz_1354.05615234375\t9\t8.66666666666667\t7.33333333333333\n+mz_1354.10009765625\t9\t7.33333333333333\t7.33333333333333\n+mz_1354.14404296875\t9.66666666666667\t9.33333333333333\t8.33333333333333\n+mz_1354.18786621094\t11\t9.66666666666667\t8\n+mz_1354.23181152344\t10.6666666666667\t8\t9.66666666666667\n+mz_1354.27575683594\t10.3333333333333\t8.66666666666667\t7.66666666666667\n+mz_1354.31970214844\t11.3333333333333\t8.33333333333333\t8.66666666666667\n+mz_1354.36364746094\t14\t8.66666666666667\t9\n+mz_1354.40759277344\t17.6666666666667\t10\t14.3333333333333\n+mz_1354.45153808594\t23.6666666666667\t12\t20.3333333333333\n+mz_1354.49548339844\t21\t13.3333333333333\t21\n+mz_1354.53942871094\t24\t14\t18.6666666666667\n+mz_1354.58337402344\t19\t11.6666666666667\t16.6666666666667\n+mz_1354.62731933594\t16.3333333333333\t11.3333333333333\t14\n+mz_1354.67126464844\t16\t9\t13\n+mz_1354.71520996094\t14.3333333333333\t8.66666666666667\t10.6666666666667\n+mz_1354.75915527344\t15\t8\t11\n+mz_1354.80310058594\t14.6666666666667\t8.33333333333333\t9.33333333333333\n+mz_1354.84704589844\t10.6666666666667\t8.66666666666667\t10\n+mz_1354.89099121094\t11\t8.66666666666667\t9\n+mz_1354.93493652344\t9.66666666666667\t8.33333333333333\t10.6666666666667\n+mz_1354.97888183594\t11.3333333333333\t8\t8\n+mz_1355.02282714844\t9.33333333333333\t9\t9.66666666666667\n+mz_1355.06677246094\t10.3333333333333\t6.66666666666667\t8.66666666666667\n+mz_1355.11083984375\t8.66666666666667\t7\t9\n+mz_1355.15478515625\t9.33333333333333\t7\t7.33333333333333\n+mz_1355.19873046875\t10\t8\t8.66666666666667\n+mz_1355.24267578125\t9.33333333333333\t8\t9.33333333333333\n+mz_1355.28662109375\t11\t7.33333333333333\t9.33333333333333\n+mz_1355.33056640625\t13\t8.33333333333333\t8.66666666666667\n+mz_1355.37451171875\t12.6666666666667\t8\t11.6666666666667\n+mz_1355.41845703125\t15.3333333333333\t8.66666666666667\t12.3333333333333\n+mz_1355.46240234375\t18.3333333333333\t10.3333333333333\t12\n+mz_1355.50634765625\t20.3333333333333\t9.33333333333333\t13.6666666666667\n+mz_1355.55029296875\t19\t12\t15\n+mz_1355.59436035156\t17\t10\t14.3333333333333\n+mz_1355.63830566406\t15\t9.66666666666667\t12.6666666666667\n+mz_1355.68225097656\t14.6666666666667\t9\t11\n+mz_1355.72619628906\t13.3333333333333\t8\t13\n+mz_1355.77014160156\t13\t9\t9.66666666666667\n+mz_1355.81408691406\t12.3333333333333\t9\t9.66666666666667\n+mz_1355.85803222656\t12\t9\t9\n+mz_1355.90209960938\t11\t9\t8.66666666666667\n+mz_1355.94604492188\t11.3333333333333\t9\t7.33333333333333\n+mz_1355.98999023438\t9.66666666666667\t8\t8.66666666666667\n+mz_1356.03393554688\t10\t9\t7.33333333333333\n+mz_1356.07788085938\t10.3333333333333\t7.66666666666667\t9\n'
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/pca_imzml.pdf
b
Binary file test-data/pca_imzml.pdf has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/picked.ibd
b
Binary file test-data/picked.ibd has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/picked.imzml
--- a/test-data/picked.imzml Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/picked.imzml Thu Apr 23 08:09:32 2020 -0400
b
@@ -8,8 +8,8 @@
  <fileDescription>
   <fileContent>
    <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
-   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{3d75db19-25c6-4579-a1bc-fb0ee0bae869}"/>
-   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="3fbb731b958a3ec73031a5894c29e3ef16586f39"/>
+   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{cb7c9edc-eee3-4159-a8a1-efdf5fc56a13}"/>
+   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="f3e61f4699108e65bb678cfbbd6208be562f11c9"/>
    <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
    <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
   </fileContent>
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/picked.imzml.txt
--- a/test-data/picked.imzml.txt Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/picked.imzml.txt Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 192
--rw-r--r-- 1 meli meli 157984 Dez 11 00:03 ibd
--rw-r--r-- 1 meli meli  35012 Dez 11 00:03 imzml
+-rw-r--r-- 1 meli meli 157984 Apr 21 12:42 ibd
+-rw-r--r-- 1 meli meli  35012 Apr 21 12:42 imzml
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/picked_QC.pdf
b
Binary file test-data/picked_QC.pdf has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/pixel_out3.tabular
--- a/test-data/pixel_out3.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/pixel_out3.tabular Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
-spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz m/z count
+spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz mz_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
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/pixel_out4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out4.tabular Thu Apr 23 08:09:32 2020 -0400
b
@@ -0,0 +1,10 @@
+spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz mz_count
+xy_1_1 1 1 1 1662 0 121.85 3.05 152.928453433486 7
+xy_2_1 2 1 2 2512 0 182.32 4.76 153.081458377151 8
+xy_3_1 3 1 3 2523 0 161.81 3.48 152.989637050972 17
+xy_1_2 1 2 4 2508 0 200.96 4.6 153.081458377151 16
+xy_2_2 2 2 5 2273 0 135.31 2.38 328.905406095478 10
+xy_3_2 3 2 6 1908 0 108.4 1.97 171.257828125883 9
+xy_1_3 1 3 7 2160 0 127.85 2.27 153.173334812658 8
+xy_2_3 2 3 8 2523 0 168.27 3.83 152.989637050972 15
+xy_3_3 3 3 9 2788 0 243.54 9.24 153.081458377151 8
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/pixels_test6.tabular
--- a/test-data/pixels_test6.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/pixels_test6.tabular Thu Apr 23 08:09:32 2020 -0400
b
@@ -2,24 +2,24 @@
 xy_1_1 1 1 A
 xy_2_1 2 1 A
 xy_3_1 3 1 B
-xy_4_1 4 1 A
-xy_1_2 1 2 A
-xy_2_2 2 2 A
+xy_4_1 4 1 C
+xy_1_2 1 2 C
+xy_2_2 2 2 C
 xy_3_2 3 2 A
 xy_4_2 4 2 A
 xy_1_3 1 3 A
 xy_2_3 2 3 B
-xy_3_3 3 3 A
+xy_3_3 3 3 C
 xy_4_3 4 3 A
-xy_10_1 10 1 A
-xy_11_1 11 1 A
-xy_12_1 12 1 A
+xy_10_1 10 1 C
+xy_11_1 11 1 C
+xy_12_1 12 1 C
 xy_13_1 13 1 B
-xy_10_2 10 2 B
+xy_10_2 10 2 C
 xy_11_2 11 2 B
-xy_12_2 12 2 A
-xy_13_2 13 2 B
-xy_10_3 10 3 A
-xy_11_3 11 3 A
+xy_12_2 12 2 C
+xy_13_2 13 2 C
+xy_10_3 10 3 C
+xy_11_3 11 3 C
 xy_12_3 12 3 B
-xy_13_3 13 3 A
+xy_13_3 13 3 C
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/preprocessing_results3.ibd
b
Binary file test-data/preprocessing_results3.ibd has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/preprocessing_results3.imzml
--- a/test-data/preprocessing_results3.imzml Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/preprocessing_results3.imzml Thu Apr 23 08:09:32 2020 -0400
b
b'@@ -9,9 +9,9 @@\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="f367e393-ca54-4bcc-bc17-10f87a3e41d0" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b9439af71c5fb6703e3fe571d12a1f9b6f90d82c" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="df9dd256-6485-4954-8338-ddb0c760d4dc" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ea9ad44f2615ef4d24b92d3ceb38dfa8ec47a978" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n \t<referenceableParamGroupList count="4">\n@@ -86,15 +86,15 @@\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="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="64" />\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="28" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\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="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="64" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -114,16 +114,16 @@\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="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="144" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\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="40" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="164" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -143,16 +143,16 @@\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'..b'00102" name="external offset" value="672" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="68" />\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="100" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="740" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="68" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -288,16 +288,16 @@\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="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="808" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\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="112" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="840" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -317,16 +317,16 @@\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="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="872" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="11" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="44" />\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="124" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="916" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="11" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="44" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n'
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/preprocessing_results3.imzml.txt
--- a/test-data/preprocessing_results3.imzml.txt Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/preprocessing_results3.imzml.txt Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli   136 Mär 24 11:10 ibd
--rw-r--r-- 1 meli meli 18088 Mär 24 11:10 imzml
+-rw-r--r-- 1 meli meli   960 Apr 22 15:36 ibd
+-rw-r--r-- 1 meli meli 18112 Apr 22 15:36 imzml
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/preprocessing_results3.pdf
b
Binary file test-data/preprocessing_results3.pdf has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/preprocessing_results5.ibd
b
Binary file test-data/preprocessing_results5.ibd has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/preprocessing_results5.imzml
--- a/test-data/preprocessing_results5.imzml Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/preprocessing_results5.imzml Thu Apr 23 08:09:32 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c88c7d70-c027-4fa3-b274-0af5e7f4d117" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="16a0f87989392c55b1c02770f15095dcf0d9408e" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="1cb5b7df-bc82-4588-9a14-1dd58a3983a7" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a16bf7a9d9d4064ce94821e3e7df2681725a497b" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/preprocessing_results5.imzml.txt
--- a/test-data/preprocessing_results5.imzml.txt Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/preprocessing_results5.imzml.txt Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 428
--rw-r--r-- 1 meli meli 415936 Mär 24 10:57 ibd
--rw-r--r-- 1 meli meli  18569 Mär 24 10:57 imzml
+-rw-r--r-- 1 meli meli 415936 Apr 19 21:07 ibd
+-rw-r--r-- 1 meli meli  18569 Apr 19 21:07 imzml
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/preprocessing_results5.pdf
b
Binary file test-data/preprocessing_results5.pdf has changed
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diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/sd_out2.tabular
--- a/test-data/sd_out2.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/sd_out2.tabular Thu Apr 23 08:09:32 2020 -0400
b
b'@@ -1,3673 +1,3673 @@\n mz name\tcol1\tcol2\tcol3\n-mz_1199.47\t9.8488578017961\t1.52752523165195\t1.15470053837925\n-mz_1199.51\t14.7309198626562\t4.72581562625261\t2.08166599946613\n-mz_1199.56\t27.4286954362276\t3.05505046330389\t7.50555349946513\n-mz_1199.6\t31.1929479209644\t8.50490054811538\t5.68624070307733\n-mz_1199.64\t20.0748598998847\t3.60555127546399\t1.52752523165195\n-mz_1199.68\t12.0968315410827\t3.05505046330389\t5.85946527708232\n-mz_1199.72\t8.38649708360608\t3.60555127546399\t3.21455025366432\n-mz_1199.76\t7.76745346515403\t2.3094010767585\t2.88675134594813\n-mz_1199.8\t7.76745346515403\t0.577350269189626\t3.21455025366432\n-mz_1199.85\t4.72581562625261\t1\t0\n-mz_1199.89\t3.60555127546399\t2.08166599946613\t2\n-mz_1199.93\t1.15470053837925\t2.3094010767585\t1.73205080756888\n-mz_1199.97\t1.52752523165195\t1.52752523165195\t1.15470053837925\n-mz_1200.01\t1.15470053837925\t1.52752523165195\t0.577350269189626\n-mz_1200.05\t0.577350269189626\t1.52752523165195\t1.15470053837925\n-mz_1200.09\t2.64575131106459\t1.52752523165195\t3.05505046330389\n-mz_1200.14\t3.05505046330389\t0\t0.577350269189626\n-mz_1200.18\t0.577350269189626\t3\t2.3094010767585\n-mz_1200.22\t1.52752523165195\t0.577350269189626\t1.52752523165195\n-mz_1200.26\t2.08166599946613\t0.577350269189626\t1.52752523165195\n-mz_1200.3\t1.15470053837925\t1.52752523165195\t1\n-mz_1200.34\t1.52752523165195\t1.15470053837925\t3.05505046330389\n-mz_1200.38\t1.52752523165195\t1.15470053837925\t1.73205080756888\n-mz_1200.42\t2.88675134594813\t1\t3.51188458428425\n-mz_1200.47\t2.64575131106459\t1\t2.08166599946613\n-mz_1200.51\t7.57187779440036\t1.52752523165195\t5.03322295684717\n-mz_1200.55\t15.5884572681199\t2.3094010767585\t3.78593889720018\n-mz_1200.59\t17.0391705588427\t5.19615242270663\t1.52752523165195\n-mz_1200.63\t13\t4.50924975282289\t4.58257569495584\n-mz_1200.67\t8.32666399786453\t1.52752523165195\t1.15470053837925\n-mz_1200.71\t6.35085296108588\t1.52752523165195\t3.21455025366432\n-mz_1200.76\t4.16333199893227\t1.15470053837925\t2\n-mz_1200.8\t2.64575131106459\t1.52752523165195\t1.15470053837925\n-mz_1200.84\t2.3094010767585\t0.577350269189626\t0\n-mz_1200.88\t3.21455025366432\t1.15470053837925\t1.15470053837925\n-mz_1200.92\t2.64575131106459\t2.08166599946613\t2.08166599946613\n-mz_1200.96\t1.73205080756888\t1\t2.3094010767585\n-mz_1201\t1.52752523165195\t1.73205080756888\t1.52752523165195\n-mz_1201.05\t1\t1.15470053837925\t0.577350269189626\n-mz_1201.09\t2.3094010767585\t1.52752523165195\t1.52752523165195\n-mz_1201.13\t1.73205080756888\t0.577350269189626\t2.64575131106459\n-mz_1201.17\t1\t1.52752523165195\t2.64575131106459\n-mz_1201.21\t0.577350269189626\t0.577350269189626\t2.08166599946613\n-mz_1201.25\t1.52752523165195\t0.577350269189626\t0\n-mz_1201.29\t1.52752523165195\t0.577350269189626\t1\n-mz_1201.33\t1.15470053837925\t2.64575131106459\t2.64575131106459\n-mz_1201.38\t2.08166599946613\t1.73205080756888\t1\n-mz_1201.42\t5.13160143944688\t3.78593889720018\t3.05505046330389\n-mz_1201.46\t2.3094010767585\t1.73205080756888\t1.15470053837925\n-mz_1201.5\t6.65832811847939\t0.577350269189626\t2.64575131106459\n-mz_1201.54\t7\t2.51661147842358\t2.64575131106459\n-mz_1201.58\t5.5075705472861\t1.52752523165195\t2\n-mz_1201.62\t3.78593889720018\t1.52752523165195\t2.64575131106459\n-mz_1201.67\t2.64575131106459\t1.52752523165195\t0.577350269189626\n-mz_1201.71\t2.64575131106459\t1\t1.52752523165195\n-mz_1201.75\t3.78593889720018\t1.73205080756888\t1.15470053837925\n-mz_1201.79\t3.21455025366432\t2\t1\n-mz_1201.83\t2.64575131106459\t0\t2.51661147842358\n-mz_1201.87\t1.52752523165195\t0\t1\n-mz_1201.91\t1.52752523165195\t1.15470053837925\t0.577350269189626\n-mz_1201.96\t1\t1.15470053837925\t1.15470053837925\n-mz_1202\t2.64575131106459\t2\t0.577350269189626\n-mz_1202.04\t2.88675134594813\t1\t1\n-mz_1202.08\t2.08166599946613\t1.73205080756888\t1.52752523165195\n-mz_1202.12\t1.15470053837925\t1.52752523165195\t0.577350269189626\n-mz_1202.16\t1\t1\t2.64575131106459\n-mz_1202.2\t2.64575131106459\t1\t1.15470053837925\n-mz_1202.25\t2.08166599946613\t1.52752523165195\t1\n-mz_1202.29\t1\t1.52752523165195\t2\n-mz_1202.33\t3\t1.52752523165195\t1.73205080756888\n-mz_1202.37\t3.78593889720018\t0.577350269189626\t3.60555127546399\n-mz_1202.41\t2.5166114'..b'.577350269189626\t0.577350269189626\t1.52752523165195\n+mz_1353.22143554688\t1.52752523165195\t0.577350269189626\t1\n+mz_1353.26538085938\t1.52752523165195\t0.577350269189626\t2.88675134594813\n+mz_1353.30932617188\t0.577350269189626\t1.52752523165195\t0\n+mz_1353.35327148438\t3\t2\t1.15470053837925\n+mz_1353.39709472656\t0.577350269189626\t1.15470053837925\t3.60555127546399\n+mz_1353.44104003906\t2\t2.08166599946613\t1\n+mz_1353.48498535156\t1\t1.15470053837925\t1.52752523165195\n+mz_1353.52893066406\t2.3094010767585\t4.04145188432738\t3.51188458428425\n+mz_1353.57287597656\t3\t1.15470053837925\t2.08166599946613\n+mz_1353.61682128906\t1.15470053837925\t3.05505046330389\t2.08166599946613\n+mz_13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b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/spectra_1_pixel.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/spectra_1_pixel.tabular Thu Apr 23 08:09:32 2020 -0400
b
@@ -0,0 +1,3 @@
+1 1
+2 2
+3 3
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/test6.pdf
b
Binary file test-data/test6.pdf has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/test6.rdata
b
Binary file test-data/test6.rdata has changed
b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/toplabels_proc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_proc.tabular Thu Apr 23 08:09:32 2020 -0400
b
@@ -0,0 +1,101 @@
+mz r k s classes centers tstatistics p.values adj.p.values
+1199 1 2 0 1 0 0 1 1
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b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/toplabels_skm.tabular
--- a/test-data/toplabels_skm.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/toplabels_skm.tabular Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,21 +1,21 @@
 mz r k cluster centers withinss betweenss
-1199.55615234375 3 3 1 81 154 3661.33333333333
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b
diff -r 82f6c2f4332d -r 4a2ac25d1063 test-data/toplabels_ssc.tabular
--- a/test-data/toplabels_ssc.tabular Wed Mar 25 05:43:05 2020 -0400
+++ b/test-data/toplabels_ssc.tabular Thu Apr 23 08:09:32 2020 -0400
b
@@ -1,51 +1,51 @@
 mz r k s classes centers tstatistics p.values adj.p.values
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