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Changeset 7:350a84ea795c (2020-04-23)

Previous changeset 6:8da3511c9467 (2020-03-25) Next changeset 8:653e66bd9eed (2020-05-13)

Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"

modified:
data_exporter.xml
macros.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

diff -r 8da3511c9467 -r 350a84ea795c data_exporter.xml
--- a/data_exporter.xml Wed Mar 25 08:07:01 2020 -0400
+++ b/data_exporter.xml Thu Apr 23 08:06:24 2020 -0400

[

b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.2">\n+<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.0">\n <description>\n exports imzML and Analyze7.5 to tabular files\n </description>\n@@ -22,22 +22,27 @@\n \n library(Cardinal)\n \n-@READING_MSIDATA_INRAM@\n+@READING_MSIDATA@\n \n+## in case RData input is MSImageSet:\n+if (class(msidata) == "MSImageSet"){\n+ msidata = as(msidata, "MSImagingExperiment")\n+ run(msidata) = "infile"\n+ }\n \n+ ## extract spectra matrix once: \n+ msidata_matrix = as.matrix(iData(msidata))\n ###################### Intensity matrix output ################################\n \n #if "int_matrix" in str($output_options).split(","):\n print("intensity matrix output")\n \n- mz_names = gsub(" = ", "_", names(features(msidata)))\n- mz_names = gsub("/", "", mz_names)\n- pixel_names = gsub(", y = ", "_", names(pixels(msidata)))\n- pixel_names = gsub(" = ", "y_", pixel_names)\n+ mz_names = paste0("mz_", mz(msidata))\n+ pixel_names = paste0("xy_", coord(msidata)\\$x, "_", coord(msidata)\\$y)\n \n- ##spectramatrix = cbind(mz_names,spectra(msidata))\n- newmatrix = rbind(c("mz_name", pixel_names), cbind(mz_names,spectra(msidata)))\n- write.table(newmatrix, file="$intensity_matrix", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\\t")\n+ write.table(\n+ rbind(c("mz_name", pixel_names), cbind(mz_names,msidata_matrix)), ##create matrix\n+ file="$intensity_matrix", quote = FALSE, row.names = FALSE, col.names=FALSE, sep = "\\t")\n ## free up RAM space in case furhter steps will be run: \n rm(newmatrix)\n gc()\n@@ -49,21 +54,18 @@\n #if "mz_tabular" in str($output_options).split(","):\n print("mz feature output")\n \n- mz_names = gsub(" = ", "_", names(features(msidata)))\n- mz_names = gsub("/", "", mz_names)\n+ full_sample_mean = apply(msidata_matrix,1,mean, na.rm=TRUE)\n+ full_sample_sd = apply(msidata_matrix,1,sd, na.rm=TRUE)\n \n- ## mean, median, sd and SEM intensity per file and mz\n- full_sample_mean = rowMeans(spectra(msidata), na.rm=TRUE)\n- full_sample_median = apply(spectra(msidata),1,median, na.rm=TRUE)\n- full_sample_sd = apply(spectra(msidata),1,sd, na.rm=TRUE)\n- full_sample_sem = full_sample_sd/full_sample_mean*100\n- ## npeaks and sum of all intensities per spectrum and mz\n- npeaks= sum(spectra(msidata)>0, na.rm=TRUE)\n- mzTIC = rowSums(spectra(msidata), na.rm=TRUE) ## calculate intensity sum for each m/z\n- peakspermz = rowSums(spectra(msidata) > 0, na.rm=TRUE) ## calculate number of intensities > 0 for each m/z (max = number of spectra)\n+ mz_df = data.frame(paste0("mz_", mz(msidata)), ##mz names\n+ mz(msidata), ##mz values\n+ full_sample_mean, ##mean\n+ apply(msidata_matrix,1,median, na.rm=TRUE), ##median\n+ full_sample_sd, ##sd\n+ full_sample_sd/full_sample_mean*100, ##SEM\n+ rowSums(msidata_matrix, na.rm=TRUE), ## calculate intensity sum for each m/z\n+ rowSums(msidata_matrix > 0, na.rm=TRUE)) ## calculate number of intensities > 0 for each m/z (max = number of spectra)\n \n- ## combine into dataframe, order is the same for all vectors\n- mz_df = data.frame(mz_names, mz(msidata), full_sample_mean, full_sample_median, full_sample_sd, full_sample_sem, mzTIC, peakspermz)\n colnames(mz_df) = c("mz_names", "mz", "sample_mean", "sample_median", "sample_sd", "sample_sem", "intensity_sum", "number_peaks")\n write.table(mz_df, file="$feature_output", quote = FALSE, row.names = FALSE'..b'pectra_df) = c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz")\n \n #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":\n \n calibrant_list = read.delim("$counting_calibrants.mz_tabular", header = $counting_calibrants.feature_header, na.strings=c("","NA"), stringsAsFactors = FALSE)\n calibrant_list = calibrant_list[,$counting_calibrants.feature_column, drop=FALSE]\n+\n ### calculate how many input calibrant m/z are valid: \n inputcalibrants = calibrant_list[calibrant_list[,1]>min(mz(msidata)) & calibrant_list[,1]<max(mz(msidata)),,drop = FALSE]\n+\n inputcalibrantmasses = inputcalibrants[,1]\n \n ##QC plot number 2) Number of calibrants per spectrum\n@@ -214,11 +207,11 @@\n \n }else{countvector = rep(0,ncol(msidata))}\n countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts\n- colnames(countdf) = c("x_values", "y_values", "m/z count")\n+ colnames(countdf) = c("x_values", "y_values", "mz_count")\n spectra_df = merge(spectra_df, countdf, by=c("x_values", "y_values"))\n \n ## sort columns to have spectra_names as rowname in first column\n- spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "m/z count")]\n+ spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "mz_count")]\n \n #end if\n #if str($tabular_annotation.load_annotation) == \'yes_annotation\':\n@@ -228,7 +221,7 @@\n \n ## sort columns to have spectra_names as rowname in first column\n #if str($counting_calibrants.pixel_with_calibrants) == "yes_calibrants":\n- spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "m/z count", "annotation")]\n+ spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "mz_count", "annotation")]\n #else\n spectra_df = spectra_df[c("spectra_names", "x_values", "y_values","pixel_order", "peaks_per_spectrum", "median_intensity", "spectrum_TIC", "maximum_intensity", "most_abundant_mz", "annotation")]\n #end if\n@@ -335,6 +328,24 @@\n <output name="feature_output" file="features_out3.tabular"/>\n <output name="pixel_output" file="pixel_out3.tabular"/>\n </test>\n+ <test expect_num_outputs="2">\n+ <expand macro="processed_infile_imzml"/>\n+ <conditional name="processed_cond">\n+ <param name="processed_file" value="processed"/>\n+ <param name="accuracy" value="100"/>\n+ <param name="units" value="ppm"/>\n+ </conditional>\n+ <param name="output_options" value="pixel_tabular,mz_tabular"/>\n+ <conditional name="counting_calibrants">\n+ <param name="pixel_with_calibrants" value="yes_calibrants"/>\n+ <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>\n+ <param name="feature_column" value="1"/>\n+ <param name="feature_header" value="False"/>\n+ <param name="plusminus_ppm" value="200"/>\n+ </conditional>\n+ <output name="feature_output" file="features_out4.tabular"/>\n+ <output name="pixel_output" file="pixel_out4.tabular"/>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n'

diff -r 8da3511c9467 -r 350a84ea795c macros.xml
--- a/macros.xml Wed Mar 25 08:07:01 2020 -0400
+++ b/macros.xml Thu Apr 23 08:06:24 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">

diff -r 8da3511c9467 -r 350a84ea795c test-data/112_auto_combined.imzml
--- a/test-data/112_auto_combined.imzml Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/112_auto_combined.imzml Thu Apr 23 08:06:24 2020 -0400

@@ -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 @@
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<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="15" />
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diff -r 8da3511c9467 -r 350a84ea795c test-data/112_auto_combined.imzml.txt
--- a/test-data/112_auto_combined.imzml.txt Wed Mar 25 08:07:01 2020 -0400
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diff -r 8da3511c9467 -r 350a84ea795c test-data/112_auto_combined_QC.pdf

Binary file test-data/112_auto_combined_QC.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/123_combined.imzml
--- a/test-data/123_combined.imzml Wed Mar 25 08:07:01 2020 -0400
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diff -r 8da3511c9467 -r 350a84ea795c test-data/123_combined.imzml.txt
--- a/test-data/123_combined.imzml.txt Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/123_combined.imzml.txt Thu Apr 23 08:06:24 2020 -0400

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imzML file:
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diff -r 8da3511c9467 -r 350a84ea795c test-data/123_combined_QC.pdf

Binary file test-data/123_combined_QC.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/123_combined_auto.imzml
--- a/test-data/123_combined_auto.imzml Wed Mar 25 08:07:01 2020 -0400
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- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="147d6aa7f71a366246c93d750fcc9240b84c748f" />
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diff -r 8da3511c9467 -r 350a84ea795c test-data/123_combined_auto.imzml.txt
--- a/test-data/123_combined_auto.imzml.txt Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/123_combined_auto.imzml.txt Thu Apr 23 08:06:24 2020 -0400

@@ -1,4 +1,4 @@
imzML file:
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diff -r 8da3511c9467 -r 350a84ea795c test-data/123_combined_auto.pdf

Binary file test-data/123_combined_auto.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/12_combined.imzml
--- a/test-data/12_combined.imzml Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/12_combined.imzml Thu Apr 23 08:06:24 2020 -0400

diff -r 8da3511c9467 -r 350a84ea795c test-data/12_combined.imzml.txt
--- a/test-data/12_combined.imzml.txt Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/12_combined.imzml.txt Thu Apr 23 08:06:24 2020 -0400

@@ -1,4 +1,4 @@
imzML file:
total 352
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--rw-r--r-- 1 meli meli 17217 Dez 11 00:07 imzml
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diff -r 8da3511c9467 -r 350a84ea795c test-data/12_combined_QC.pdf

Binary file test-data/12_combined_QC.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/2123_auto_combined.imzml
--- a/test-data/2123_auto_combined.imzml Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/2123_auto_combined.imzml Thu Apr 23 08:06:24 2020 -0400

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diff -r 8da3511c9467 -r 350a84ea795c test-data/2123_auto_combined.imzml.txt
--- a/test-data/2123_auto_combined.imzml.txt Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/2123_auto_combined.imzml.txt Thu Apr 23 08:06:24 2020 -0400

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imzML file:
total 656
--rw-r--r-- 1 meli meli 638340 Dez 11 00:12 ibd
--rw-r--r-- 1 meli meli 30107 Dez 11 00:12 imzml
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diff -r 8da3511c9467 -r 350a84ea795c test-data/Heatmaps_processed.pdf

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diff -r 8da3511c9467 -r 350a84ea795c test-data/centroids_proc.pdf

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diff -r 8da3511c9467 -r 350a84ea795c test-data/classes_proc.tabular
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diff -r 8da3511c9467 -r 350a84ea795c test-data/classes_ssc.tabular
--- a/test-data/classes_ssc.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/classes_ssc.tabular Thu Apr 23 08:06:24 2020 -0400

@@ -1,10 +1,10 @@
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diff -r 8da3511c9467 -r 350a84ea795c test-data/cluster_skm.RData

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diff -r 8da3511c9467 -r 350a84ea795c test-data/cluster_skm.tabular
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diff -r 8da3511c9467 -r 350a84ea795c test-data/features_out1.tabular
--- a/test-data/features_out1.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/features_out1.tabular Thu Apr 23 08:06:24 2020 -0400

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'

diff -r 8da3511c9467 -r 350a84ea795c test-data/features_out3.tabular
--- a/test-data/features_out3.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/features_out3.tabular Thu Apr 23 08:06:24 2020 -0400

diff -r 8da3511c9467 -r 350a84ea795c test-data/features_out4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_out4.tabular Thu Apr 23 08:06:24 2020 -0400

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_795.18134288471\t795.18134288471\t1.03806936143277e-05\t0\t2.06207299669125e-05\t198.645010950437\t9.34262425289489e-05\t3\n+mz_795.340395058504\t795.340395058504\t4.27814623233442e-06\t0\t8.1280368419713e-06\t189.989691809486\t3.85033160910098e-05\t4\n+mz_795.499479045915\t795.499479045915\t1.34739204642958e-06\t0\t4.04217613928874e-06\t300\t1.21265284178662e-05\t1\n+mz_795.658594853305\t795.658594853305\t2.41733044100319e-07\t0\t7.24443858335399e-07\t299.687558658615\t2.17559739690287e-06\t3\n+mz_795.817742487039\t795.817742487039\t6.82981933354378e-10\t0\t1.46305214500577e-09\t214.215350883467\t6.1468374001894e-09\t3\n+mz_795.976921953483\t795.976921953483\t1.97925830865682e-10\t0\t4.47965241832071e-10\t226.329852891245\t1.78133247779114e-09\t3\n+mz_796.136133259004\t796.136133259004\t4.59929004603676e-11\t0\t1.37978701381103e-10\t300\t4.13936104143309e-10\t1\n+mz_796.295376409971\t796.295376409971\t4.93382472915889e-14\t0\t9.79336915953797e-14\t198.494468229874\t4.440442256243e-13\t3\n+mz_796.454651412753\t796.454651412753\t2.04924542989995e-14\t0\t3.94621959061835e-14\t192.56939813261\t1.84432088690996e-13\t3\n+mz_796.613958273722\t796.613958273722\t0.0640500783920358\t0\t0.192150235176084\t299.999999999963\t0.576450705528322\t2\n+mz_796.773296999249\t796.773296999249\t0.0406853891909122\t0\t0.122056167572737\t300\t0.36616850271821\t3\n+mz_796.932667595709\t796.932667595709\t1.45479372341066e-18\t0\t3.89552090887857e-18\t267.771357972718\t1.30931435106959e-17\t2\n+mz_797.092070069475\t797.092070069475\t3.53827797679273e-07\t0\t1.06148339303488e-06\t299.99999999917\t3.18445017911345e-06\t2\n+mz_797.251504426925\t797.251504426925\t4.13144920862074e-06\t0\t1.23943476258622e-05\t299.999999999999\t3.71830428775867e-05\t2\n+mz_797.410970674435\t797.410970674435\t1.09320730403953e-06\t0\t3.27962191211858e-06\t300\t9.83886573635573e-06\t3\n+mz_797.570468818384\t797.570468818384\t9.69305316816355e-23\t0\t1.9109331645976e-22\t197.144607735567\t8.7237478513472e-22\t3\n+mz_797.729998865153\t797.729998865153\t3.54466308157491e-10\t0\t1.06339892447237e-09\t299.999999999971\t3.19019677341742e-09\t2\n+mz_797.889560821122\t797.889560821122\t0.0289176803618284\t0\t0.086753040485471\t299.999997925095\t0.260259123256456\t3\n+mz_798.049154692673\t798.049154692673\t0.0374488714668486\t0\t0.112346614400546\t300\t0.337039843201637\t3\n+mz_798.208780486191\t798.208780486191\t0.000266989253263465\t0\t0.000800967759759802\t299.999999988541\t0.00240290327937119\t3\n+mz_798.368438208061\t798.368438208061\t2.34458102407087e-14\t0\t7.0337430722126e-14\t299.999999999999\t2.11012292166378e-13\t2\n+mz_798.528127864668\t798.528127864668\t0.00141713557604831\t0\t0.0042384206336443\t299.083637817008\t0.0127542201844348\t4\n+mz_798.687849462401\t798.687849462401\t0.181158882302081\t0\t0.543476171075702\t299.999737340761\t1.63042994071873\t4\n+mz_798.847603007648\t798.847603007648\t0.0144867946704229\t0\t0.0434603840112686\t300\t0.130381152033806\t3\n+mz_799.007388506799\t799.007388506799\t2.4237529276071e-10\t0\t7.27125877994982e-10\t299.999999881527\t2.18137763484639e-09\t3\n+mz_799.167205966246\t799.167205966246\t3.01763521578143e-11\t0\t9.05290564734429e-11\t300\t2.71587169420329e-10\t3\n+mz_799.327055392382\t799.327055392382\t1.10960895597907e-05\t0\t3.32882668224669e-05\t299.999983265229\t9.98648060381163e-05\t4\n+mz_799.486936791601\t799.486936791601\t2.06164372684725e-07\t0\t6.18493118054175e-07\t300\t1.85547935416253e-06\t3\n+mz_799.646850170297\t799.646850170297\t0.051657970580808\t0\t0.154973911742362\t299.999999999881\t0.464921735227272\t4\n+mz_799.806795534868\t799.806795534868\t0.0394212479392693\t0\t0.118263743817806\t299.999999999995\t0.354791231453424\t2\n+mz_799.96677289171\t799.96677289171\t8.54203856374182e-27\t0\t2.56261156912255e-26\t300\t7.68783470736764e-26\t1\n'

diff -r 8da3511c9467 -r 350a84ea795c test-data/features_test6.tabular
--- a/test-data/features_test6.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/features_test6.tabular Thu Apr 23 08:06:24 2020 -0400

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'

diff -r 8da3511c9467 -r 350a84ea795c test-data/int_matrix1.tabular
--- a/test-data/int_matrix1.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/int_matrix1.tabular Thu Apr 23 08:06:24 2020 -0400

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'

diff -r 8da3511c9467 -r 350a84ea795c test-data/int_matrix3.tabular
--- a/test-data/int_matrix3.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/int_matrix3.tabular Thu Apr 23 08:06:24 2020 -0400

diff -r 8da3511c9467 -r 350a84ea795c test-data/kmeans_analyze.pdf

Binary file test-data/kmeans_analyze.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/mean_out2.tabular
--- a/test-data/mean_out2.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/mean_out2.tabular Thu Apr 23 08:06:24 2020 -0400

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'

diff -r 8da3511c9467 -r 350a84ea795c test-data/pca_imzml.pdf

Binary file test-data/pca_imzml.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/picked.ibd

Binary file test-data/picked.ibd has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/picked.imzml
--- a/test-data/picked.imzml Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/picked.imzml Thu Apr 23 08:06:24 2020 -0400

@@ -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>

diff -r 8da3511c9467 -r 350a84ea795c test-data/picked.imzml.txt
--- a/test-data/picked.imzml.txt Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/picked.imzml.txt Thu Apr 23 08:06:24 2020 -0400

@@ -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

diff -r 8da3511c9467 -r 350a84ea795c test-data/picked_QC.pdf

Binary file test-data/picked_QC.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/pixel_out3.tabular
--- a/test-data/pixel_out3.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/pixel_out3.tabular Thu Apr 23 08:06:24 2020 -0400

@@ -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

diff -r 8da3511c9467 -r 350a84ea795c test-data/pixel_out4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pixel_out4.tabular Thu Apr 23 08:06:24 2020 -0400

@@ -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

diff -r 8da3511c9467 -r 350a84ea795c test-data/pixels_test6.tabular
--- a/test-data/pixels_test6.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/pixels_test6.tabular Thu Apr 23 08:06:24 2020 -0400

@@ -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

diff -r 8da3511c9467 -r 350a84ea795c test-data/preprocessing_results3.ibd

Binary file test-data/preprocessing_results3.ibd has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/preprocessing_results3.imzml
--- a/test-data/preprocessing_results3.imzml Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/preprocessing_results3.imzml Thu Apr 23 08:06:24 2020 -0400

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 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diff -r 8da3511c9467 -r 350a84ea795c test-data/preprocessing_results3.imzml.txt
--- a/test-data/preprocessing_results3.imzml.txt Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/preprocessing_results3.imzml.txt Thu Apr 23 08:06:24 2020 -0400

@@ -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

diff -r 8da3511c9467 -r 350a84ea795c test-data/preprocessing_results3.pdf

Binary file test-data/preprocessing_results3.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/preprocessing_results5.ibd

Binary file test-data/preprocessing_results5.ibd has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/preprocessing_results5.imzml
--- a/test-data/preprocessing_results5.imzml Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/preprocessing_results5.imzml Thu Apr 23 08:06:24 2020 -0400

diff -r 8da3511c9467 -r 350a84ea795c test-data/preprocessing_results5.imzml.txt
--- a/test-data/preprocessing_results5.imzml.txt Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/preprocessing_results5.imzml.txt Thu Apr 23 08:06:24 2020 -0400

@@ -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

diff -r 8da3511c9467 -r 350a84ea795c test-data/preprocessing_results5.pdf

Binary file test-data/preprocessing_results5.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/sd_out2.tabular
--- a/test-data/sd_out2.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/sd_out2.tabular Thu Apr 23 08:06:24 2020 -0400

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_1353.66076660156\t4.16333199893227\t0.577350269189626\t2.64575131106459\n+mz_1353.70458984375\t2.3094010767585\t2.3094010767585\t3.21455025366432\n+mz_1353.74853515625\t1.15470053837925\t1.15470053837925\t1.15470053837925\n+mz_1353.79248046875\t1\t1.15470053837925\t2.08166599946613\n+mz_1353.83642578125\t3.46410161513775\t0.577350269189626\t1\n+mz_1353.88037109375\t1\t2.08166599946613\t1.15470053837925\n+mz_1353.92431640625\t0.577350269189626\t1.15470053837925\t2\n+mz_1353.96826171875\t1\t1.52752523165195\t0.577350269189626\n+mz_1354.01220703125\t0.577350269189626\t0.577350269189626\t2.08166599946613\n+mz_1354.05615234375\t1\t2.08166599946613\t0.577350269189626\n+mz_1354.10009765625\t1\t0.577350269189626\t1.52752523165195\n+mz_1354.14404296875\t0.577350269189626\t1.52752523165195\t0.577350269189626\n+mz_1354.18786621094\t1\t0.577350269189626\t2\n+mz_1354.23181152344\t3.78593889720018\t1\t1.15470053837925\n+mz_1354.27575683594\t0.577350269189626\t1.52752523165195\t0.577350269189626\n+mz_1354.31970214844\t1.52752523165195\t0.577350269189626\t0.577350269189626\n+mz_1354.36364746094\t1\t0.577350269189626\t1.73205080756888\n+mz_1354.40759277344\t2.88675134594813\t1\t2.08166599946613\n+mz_1354.45153808594\t3.21455025366432\t3\t2.3094010767585\n+mz_1354.49548339844\t1\t2.3094010767585\t1\n+mz_1354.53942871094\t3.60555127546399\t2\t3.21455025366432\n+mz_1354.58337402344\t1.73205080756888\t2.08166599946613\t0.577350269189626\n+mz_1354.62731933594\t1.52752523165195\t1.52752523165195\t1\n+mz_1354.67126464844\t2\t2.64575131106459\t1\n+mz_1354.71520996094\t1.15470053837925\t0.577350269189626\t1.15470053837925\n+mz_1354.75915527344\t1.73205080756888\t3.46410161513775\t1\n+mz_1354.80310058594\t1.15470053837925\t1.52752523165195\t0.577350269189626\n+mz_1354.84704589844\t1.15470053837925\t0.577350269189626\t1\n+mz_1354.89099121094\t1.73205080756888\t0.577350269189626\t1\n+mz_1354.93493652344\t2.08166599946613\t0.577350269189626\t0.577350269189626\n+mz_1354.97888183594\t1.52752523165195\t1\t2\n+mz_1355.02282714844\t1.15470053837925\t1\t0.577350269189626\n+mz_1355.06677246094\t0.577350269189626\t2.08166599946613\t0.577350269189626\n+mz_1355.11083984375\t1.15470053837925\t2\t1\n+mz_1355.15478515625\t0.577350269189626\t0\t0.577350269189626\n+mz_1355.19873046875\t0\t1.73205080756888\t1.52752523165195\n+mz_1355.24267578125\t1.15470053837925\t2\t0.577350269189626\n+mz_1355.28662109375\t2\t0.577350269189626\t0.577350269189626\n+mz_1355.33056640625\t1.73205080756888\t0.577350269189626\t2.08166599946613\n+mz_1355.37451171875\t0.577350269189626\t1\t1.15470053837925\n+mz_1355.41845703125\t3.78593889720018\t2.51661147842358\t2.3094010767585\n+mz_1355.46240234375\t3.21455025366432\t3.51188458428425\t1.73205080756888\n+mz_1355.50634765625\t2.51661147842358\t1.52752523165195\t1.52752523165195\n+mz_1355.55029296875\t1\t2.64575131106459\t3.60555127546399\n+mz_1355.59436035156\t1\t1\t3.05505046330389\n+mz_1355.63830566406\t1\t2.08166599946613\t1.52752523165195\n+mz_1355.68225097656\t2.88675134594813\t1\t1\n+mz_1355.72619628906\t2.08166599946613\t0\t4.58257569495584\n+mz_1355.77014160156\t2\t0\t0.577350269189626\n+mz_1355.81408691406\t0.577350269189626\t1\t0.577350269189626\n+mz_1355.85803222656\t1\t1.73205080756888\t1\n+mz_1355.90209960938\t1\t1.73205080756888\t1.15470053837925\n+mz_1355.94604492188\t2.51661147842358\t1\t0.577350269189626\n+mz_1355.98999023438\t1.15470053837925\t1.73205080756888\t1.15470053837925\n+mz_1356.03393554688\t1.73205080756888\t0\t1.52752523165195\n+mz_1356.07788085938\t1.52752523165195\t2.08166599946613\t1\n'

diff -r 8da3511c9467 -r 350a84ea795c 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 08:06:24 2020 -0400

@@ -0,0 +1,3 @@
+1 1
+2 2
+3 3

diff -r 8da3511c9467 -r 350a84ea795c test-data/test6.pdf

Binary file test-data/test6.pdf has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/test6.rdata

Binary file test-data/test6.rdata has changed

diff -r 8da3511c9467 -r 350a84ea795c test-data/toplabels_proc.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toplabels_proc.tabular Thu Apr 23 08:06:24 2020 -0400

@@ -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
+1200 1 2 0 1 3.06556174490187 0 1 1
+1201 1 2 0 1 1.24045880635579 0 1 1
+1202 1 2 0 1 0.269693666034275 0 1 1
+1203 1 2 0 1 0 0 1 1
+1204 1 2 0 1 0 0 1 1
+1205 1 2 0 1 0 0 1 1
+1206 1 2 0 1 0 0 1 1
+1207 1 2 0 1 0 0 1 1
+1208 1 2 0 1 0 0 1 1
+1209 1 2 0 1 1.43794178962708 0 1 1
+1210 1 2 0 1 0.82622406217787 0 1 1
+1211 1 2 0 1 0.249723381466336 0 1 1
+1212 1 2 0 1 0 0 1 1
+1213 1 2 0 1 0 0 1 1
+1214 1 2 0 1 0.247201071845161 0 1 1
+1215 1 2 0 1 0.517291307449341 0 1 1
+1216 1 2 0 1 0 0 1 1
+1217 1 2 0 1 0 0 1 1
+1218 1 2 0 1 0 0 1 1
+1219 1 2 0 1 0 0 1 1
+1220 1 2 0 1 0.278993447621663 0 1 1
+1221 1 2 0 1 0 0 1 1
+1222 1 2 0 1 0.241794321272108 0 1 1
+1223 1 2 0 1 1.01245986090766 0 1 1
+1224 1 2 0 1 0.803900904125638 0 1 1
+1225 1 2 0 1 0.456217077043321 0 1 1
+1226 1 2 0 1 0 0 1 1
+1227 1 2 0 1 0 0 1 1
+1228 1 2 0 1 0 0 1 1
+1229 1 2 0 1 0 0 1 1
+1230 1 2 0 1 0 0 1 1
+1231 1 2 0 1 0 0 1 1
+1232 1 2 0 1 0 0 1 1
+1233 1 2 0 1 0 0 1 1
+1234 1 2 0 1 0 0 1 1
+1235 1 2 0 1 0 0 1 1
+1236 1 2 0 1 0 0 1 1
+1237 1 2 0 1 0 0 1 1
+1238 1 2 0 1 0 0 1 1
+1239 1 2 0 1 0 0 1 1
+1240 1 2 0 1 0.517177846696642 0 1 1
+1241 1 2 0 1 0 0 1 1
+1242 1 2 0 1 0 0 1 1
+1243 1 2 0 1 0 0 1 1
+1244 1 2 0 1 0.220909158388774 0 1 1
+1245 1 2 0 1 0.441907816463047 0 1 1
+1246 1 2 0 1 0 0 1 1
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+1252 1 2 0 1 0 0 1 1
+1253 1 2 0 1 0 0 1 1
+1254 1 2 0 1 0 0 1 1
+1255 1 2 0 1 0 0 1 1
+1256 1 2 0 1 0 0 1 1
+1257 1 2 0 1 0 0 1 1
+1258 1 2 0 1 0 0 1 1
+1259 1 2 0 1 0 0 1 1
+1260 1 2 0 1 0 0 1 1
+1261 1 2 0 1 0.32789675394694 0 1 1
+1262 1 2 0 1 0.268932872348362 0 1 1
+1263 1 2 0 1 0 0 1 1
+1264 1 2 0 1 2.64317909876506 0 1 1
+1265 1 2 0 1 1.4933132065667 0 1 1
+1266 1 2 0 1 0 0 1 1
+1267 1 2 0 1 0.584092458089193 0 1 1
+1268 1 2 0 1 2.51373351944817 0 1 1
+1269 1 2 0 1 1.80340676837497 0 1 1
+1270 1 2 0 1 0 0 1 1
+1271 1 2 0 1 0 0 1 1
+1272 1 2 0 1 0 0 1 1
+1273 1 2 0 1 0 0 1 1
+1274 1 2 0 1 0 0 1 1
+1275 1 2 0 1 0 0 1 1
+1276 1 2 0 1 0 0 1 1
+1277 1 2 0 1 0 0 1 1
+1278 1 2 0 1 0 0 1 1
+1279 1 2 0 1 0 0 1 1
+1280 1 2 0 1 0 0 1 1
+1281 1 2 0 1 0.250744581222534 0 1 1
+1282 1 2 0 1 0.760214355256822 0 1 1
+1283 1 2 0 1 0 0 1 1
+1284 1 2 0 1 0 0 1 1
+1285 1 2 0 1 0 0 1 1
+1286 1 2 0 1 0 0 1 1
+1287 1 2 0 1 0.238297859827677 0 1 1
+1288 1 2 0 1 0 0 1 1
+1289 1 2 0 1 1.15708703464932 0 1 1
+1290 1 2 0 1 1.00530293252733 0 1 1
+1291 1 2 0 1 0.249645392100016 0 1 1
+1292 1 2 0 1 0 0 1 1
+1293 1 2 0 1 0 0 1 1
+1294 1 2 0 1 0 0 1 1
+1295 1 2 0 1 0 0 1 1
+1296 1 2 0 1 0.231536282433404 0 1 1
+1297 1 2 0 1 2.14849718411764 0 1 1
+1298 1 2 0 1 0.742050197389391 0 1 1

diff -r 8da3511c9467 -r 350a84ea795c test-data/toplabels_skm.tabular
--- a/test-data/toplabels_skm.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/toplabels_skm.tabular Thu Apr 23 08:06:24 2020 -0400

@@ -1,21 +1,21 @@
mz r k cluster centers withinss betweenss
-1199.55615234375 3 3 1 81 154 3661.33333333333
-1199.55615234375 3 3 2 12.3333333333333 18.6666666666667 3661.33333333333
-1199.55615234375 3 3 3 37 0 3661.33333333333
-1199.59753417969 3 3 1 84 137.2 3658.13333333333
-1199.59753417969 3 3 2 14.3333333333333 144.666666666667 3658.13333333333
-1199.59753417969 3 3 3 34.6 0 3658.13333333333
-1199.55615234375 1 3 1 49.3333333333333 1504.66666666667 2198
-1199.55615234375 1 3 2 12.3333333333333 112.666666666667 2198
-1199.55615234375 1 3 3 39.3333333333333 18.6666666666667 2198
-1199.55615234375 2 3 1 49.3333333333333 1504.66666666667 2198
-1199.55615234375 2 3 2 12.3333333333333 112.666666666667 2198
-1199.55615234375 2 3 3 39.3333333333333 18.6666666666667 2198
-1199.63891601562 3 3 1 62 45.2 2049.02222222222
-1199.63891601562 3 3 2 11 26 2049.02222222222
-1199.63891601562 3 3 3 30.4 0 2049.02222222222
-1199.55615234375 2 2 1 44.3333333333333 1767.33333333333 2048
-1199.55615234375 2 2 2 12.3333333333333 18.6666666666667 2048
-1199.55615234375 3 2 1 44.3333333333333 1767.33333333333 2048
-1199.55615234375 3 2 2 12.3333333333333 18.6666666666667 2048
-1199.59753417969 1 3 1 48 1946 1784.66666666667
+329.083343505859 1 3 1 0.708310013016065 0 3.15454318073589
+329.083343505859 1 3 2 2.06111800670624 0.348399350284836 3.15454318073589
+329.083343505859 1 3 3 1.72517621517181 0.549843039511264 3.15454318073589
+329.083343505859 2 3 1 0.708310013016065 0 3.15454318073589
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+329.083343505859 2 3 3 1.72517621517181 0.549843039511264 3.15454318073589
+329.083343505859 3 3 1 0.708310013016065 0 3.15454318073589
+329.083343505859 3 3 2 2.06111800670624 0.348399350284836 3.15454318073589
+329.083343505859 3 3 3 1.72517621517181 0.549843039511264 3.15454318073589
+329 1 3 1 0.982837170362473 0 3.09113153043007
+329 1 3 2 2.40426647663116 0.0706077629095319 3.09113153043007
+329 1 3 3 1.07743680477142 0.879613918408614 3.09113153043007
+329 2 3 1 0.982837170362473 0 3.09113153043007
+329 2 3 2 2.40426647663116 0.0706077629095319 3.09113153043007
+329 2 3 3 1.07743680477142 0.879613918408614 3.09113153043007
+329 3 3 1 0.982837170362473 0 3.09113153043007
+329 3 3 2 2.40426647663116 0.0706077629095319 3.09113153043007
+329 3 3 3 1.07743680477142 0.879613918408614 3.09113153043007
+329 1 2 1 0.996351403849466 0.887284567691734 3.08346088114695
+329 1 2 2 2.40426647663116 0.0706077629095319 3.08346088114695

diff -r 8da3511c9467 -r 350a84ea795c test-data/toplabels_ssc.tabular
--- a/test-data/toplabels_ssc.tabular Wed Mar 25 08:07:01 2020 -0400
+++ b/test-data/toplabels_ssc.tabular Thu Apr 23 08:06:24 2020 -0400

@@ -1,51 +1,51 @@
mz r k s classes centers tstatistics p.values adj.p.values
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-200.25 2 3 2 1 10.4880169699887 0.449474897701911 NA NA
-200.333343505859 1 3 2 1 10.2892503590812 0.449474610932727 NA NA
-200.333343505859 2 3 2 1 10.2892503590812 0.449474610932727 NA NA
-259.833343505859 1 3 2 1 9.55638913925806 0.449473448172064 NA NA
-259.833343505859 2 3 2 1 9.55638913925806 0.449473448172064 NA NA
-360.916687011719 1 3 2 1 9.04224883162212 0.449472524177856 NA NA
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-200.16667175293 1 3 2 1 6.16326174971333 0.449464481313509 NA NA
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-225 1 3 2 1 5.71436916011582 0.449462496977867 NA NA
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-364.416687011719 1 3 2 1 4.30740701190317 0.449453597945591 NA NA
-364.416687011719 2 3 2 1 4.30740701190317 0.449453597945591 NA NA
-370 1 3 2 1 4.15967192336677 0.449452314295502 NA NA
-370 2 3 2 1 4.15967192336677 0.449452314295502 NA NA
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-249.333343505859 2 3 2 1 4.06900916364662 0.449451480388054 NA NA
-260 1 3 2 1 4.06636831188445 0.449451455520709 NA NA
-260 2 3 2 1 4.06636831188445 0.449451455520709 NA NA
-361 1 3 2 1 3.70261707034987 0.449447694373555 NA NA
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-250.583343505859 1 3 2 1 3.44558838817237 0.449444557922452 NA NA
-250.583343505859 2 3 2 1 3.44558838817237 0.449444557922452 NA NA
-360.833343505859 1 3 2 1 3.35278414565422 0.449443307303055 NA NA
-360.833343505859 2 3 2 1 3.35278414565422 0.449443307303055 NA NA
-370.166687011719 1 3 2 1 2.82853938684749 0.449434701602457 NA NA
-370.166687011719 2 3 2 1 2.82853938684749 0.449434701602457 NA NA
-367.666687011719 1 3 2 1 2.5012261861986 0.449427499520948 NA NA
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-225.083343505859 1 3 2 1 2.45608703725853 0.449426355692286 NA NA
-225.083343505859 2 3 2 1 2.45608703725853 0.449426355692286 NA NA
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