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

Changeset 6:25b83cbd596a (2020-03-25)
Previous changeset 5:4a05e47cd0ea (2019-12-13) Next changeset 7:5e6f8fb2df07 (2020-04-23)
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
modified:
macros.xml
test-data/Analyze75.hdr
test-data/Analyze75.img
test-data/Analyze75.t2m
test-data/Example_Continuous.ibd
test-data/Example_Continuous.imzML
test-data/analyze75_filtered2.pdf
test-data/imzml_filtered3.pdf
test-data/imzml_filtered4.pdf
test-data/imzml_filtered5.pdf
test-data/out3.ibd
test-data/out3.imzml
test-data/out3.imzml.txt
test-data/out4.ibd
test-data/out4.imzml
test-data/out4.imzml.txt
test-data/out5.ibd
test-data/out5.imzml
test-data/out5.imzml.txt
test-data/out6.ibd
test-data/out6.imzml
test-data/out6.imzml.txt
test-data/out7.ibd
test-data/out7.imzml
test-data/out7.imzml.txt
test-data/preprocessing_results1.ibd
test-data/preprocessing_results1.imzml
test-data/preprocessing_results1.imzml.txt
test-data/preprocessing_results1.pdf
test-data/preprocessing_results2.ibd
test-data/preprocessing_results2.imzml
test-data/preprocessing_results2.imzml.txt
test-data/preprocessing_results2.pdf
test-data/preprocessing_results3.ibd
test-data/preprocessing_results3.imzml
test-data/preprocessing_results3.imzml.txt
test-data/preprocessing_results3.pdf
test-data/preprocessing_results4.ibd
test-data/preprocessing_results4.imzml
test-data/preprocessing_results4.imzml.txt
test-data/preprocessing_results4.pdf
test-data/preprocessing_results5.pdf
test-data/rdata_notfiltered.pdf
added:
test-data/imzml_filtered8.pdf
test-data/out8.ibd
test-data/out8.imzml
test-data/out8.imzml.txt
test-data/preprocessing_results5.ibd
test-data/preprocessing_results5.imzml
test-data/preprocessing_results5.imzml.txt
removed:
test-data/preprocessing_results5.RData
b
diff -r 4a05e47cd0ea -r 25b83cbd596a macros.xml
--- a/macros.xml Fri Dec 13 13:51:29 2019 -0500
+++ b/macros.xml Wed Mar 25 05:31:15 2020 -0400
[
b'@@ -1,316 +1,322 @@\n-<macros>\r\n-    <token name="@VERSION@">1.12.1</token>\r\n-\r\n-    <xml name="requirements">\r\n-        <requirements>\r\n-            <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>\r\n-            <requirement type="package" version="3.5.1">r-base</requirement>\r\n-            <yield/>\r\n-        </requirements>\r\n-    </xml>\r\n-\r\n-    <xml name="print_version">\r\n-        <version_command><![CDATA[\r\n-echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\\$otherPkgs\\$Cardinal\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\r\n-        ]]></version_command>\r\n-    </xml>\r\n-\r\n-    <token name="@INPUT_LINKING@"><![CDATA[\r\n-        #if $infile.ext == \'imzml\'\r\n-            ln -s \'${infile.extra_files_path}/imzml\' infile.imzML &&\r\n-            ln -s \'${infile.extra_files_path}/ibd\' infile.ibd &&\r\n-        #elif $infile.ext == \'analyze75\'\r\n-            ln -s \'${infile.extra_files_path}/hdr\' infile.hdr &&\r\n-            ln -s \'${infile.extra_files_path}/img\' infile.img &&\r\n-            ln -s \'${infile.extra_files_path}/t2m\' infile.t2m &&\r\n-        #else\r\n-            ln -s $infile infile.RData &&\r\n-        #end if\r\n-    ]]></token>\r\n-\r\n-\r\n-    <token name="@READING_MSIDATA@"><![CDATA[\r\n-        ## importing MSI data files\r\n-\r\n-        ## function to read RData files independent of filename\r\n-        loadRData <- function(fileName){\r\n-        load(fileName)\r\n-        get(ls()[ls() != "fileName"])\r\n-        }\r\n-\r\n-        #if $infile.ext == \'imzml\'\r\n-            #if str($processed_cond.processed_file) == "processed":\r\n-                msidata <- readImzML(\'infile\', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE)\r\n-                centroided(msidata) = $centroids\r\n-            #else\r\n-                msidata <- readImzML(\'infile\', attach.only=TRUE)\r\n-                centroided(msidata) = $centroids\r\n-            #end if\r\n-        #elif $infile.ext == \'analyze75\'\r\n-            msidata = readAnalyze(\'infile\', attach.only=TRUE)\r\n-            centroided(msidata) = $centroids\r\n-        #else\r\n-            msidata = loadRData(\'infile.RData\')\r\n-        #end if\r\n-\r\n-    ]]></token>\r\n-\r\n-    <token name="@DATA_PROPERTIES@"><![CDATA[\r\n-        ## Number of features (mz)\r\n-        maxfeatures = length(features(msidata))\r\n-        ## Range mz\r\n-        minmz = round(min(mz(msidata)), digits=2)\r\n-        maxmz = round(max(mz(msidata)), digits=2)\r\n-        ## Number of spectra (pixels)\r\n-        pixelcount = length(pixels(msidata))\r\n-        ## Range x coordinates\r\n-        minimumx = min(coord(msidata)[,1])\r\n-        maximumx = max(coord(msidata)[,1])\r\n-        ## Range y coordinates\r\n-        minimumy = min(coord(msidata)[,2])\r\n-        maximumy = max(coord(msidata)[,2])\r\n-\r\n-\r\n-        properties = c("Number of m/z features",\r\n-                       "Range of m/z values",\r\n-                       "Number of pixels", \r\n-                       "Range of x coordinates", \r\n-                       "Range of y coordinates")\r\n-\r\n-        values = c(paste0(maxfeatures), \r\n-                   paste0(minmz, " - ", maxmz), \r\n-                   paste0(pixelcount), \r\n-                   paste0(minimumx, " - ", maximumx),\r\n-                   paste0(minimumy, " - ", maximumy))\r\n-\r\n-        property_df = data.frame(properties, values)\r\n-    ]]></token>\r\n-\r\n-    <token name="@READING_MSIDATA_INRAM@"><![CDATA[\r\n-        ## importing MSI data files\r\n-\r\n-        ## function to read RData files independent of filename\r\n-        loadRData <- function(fileName){\r\n-        load(fileName)\r\n-        get(ls()[ls() != "fileName"])\r\n-        }\r\n-\r\n-        #if $infile.ext == \'imzml\'\r\n-            #if str($processed_cond.processed_file) == "processed":\r\n-                msidata <- readImzML(\'infile\', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")\r\n-                centroi'..b'"radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">\n+                    <option value="mz" >mz</option>\n+                    <option value="ppm" selected="True" >ppm</option>\n+                </param>\n+            </when>\n+        </conditional>\n+    </xml>\n+\n+    <xml name="pdf_filename">\n+        <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">\n+            <sanitizer invalid_char="">\n+                <valid initial="string.ascii_letters,string.digits">\n+                    <add value="_"/>\n+                    <add value=" "/>\n+                </valid>\n+            </sanitizer>\n+        </param>\n+    </xml>\n+\n+    <xml name="sanitizer_multiple_digits">\n+        <sanitizer invalid_char="">\n+            <valid initial="string.digits">\n+                <add value=":" />\n+                <add value="," />\n+            </valid>\n+        </sanitizer>\n+    </xml>\n+\n+    <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features">\n+        <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>\n+        <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>\n+        <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+    </xml>\n+\n+    <xml name="reading_2_column_mz_tabular" token_optional="false">\n+        <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"\n+            label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/>\n+        <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>\n+        <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>\n+        <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+    </xml>\n+\n+    <xml name="reading_pixel_annotations">\n+                <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"\n+                help="Tabular file with three columns: x values, y values and pixel annotations"/>\n+                <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>\n+                <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>\n+                <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>\n+                <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+    </xml>\n+\n+    <xml name="citations">\n+        <citations>\n+            <citation type="doi">10.1093/bioinformatics/btv146</citation>\n+        </citations>\n+    </xml>\n+    <xml name="infile_analyze75">\n+        <param name="infile" value="" ftype="analyze75">\n+            <composite_data value="Analyze75.hdr"/>\n+            <composite_data value="Analyze75.img"/>\n+            <composite_data value="Analyze75.t2m"/>\n+        </param>\n+    </xml>\n+    <xml name="infile_imzml">\n+        <param name="infile" value="" ftype="imzml">\n+            <composite_data value="Example_Continuous.imzML"/>\n+            <composite_data value="Example_Continuous.ibd"/>\n+        </param>\n+    </xml>\n+    <xml name="processed_infile_imzml">\n+        <param name="infile" value="" ftype="imzml">\n+            <composite_data value="Example_Processed.imzML"/>\n+            <composite_data value="Example_Processed.ibd"/>\n+        </param>\n+    </xml>\n+</macros>\n'
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/analyze75_filtered2.pdf
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/imzml_filtered3.pdf
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/imzml_filtered4.pdf
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/imzml_filtered5.pdf
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/imzml_filtered8.pdf
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out3.ibd
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out3.imzml
--- a/test-data/out3.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out3.imzml Wed Mar 25 05:31:15 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{AEDF2DEE-A321-4DAF-B971-943AE2AF79A6}" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="8311A159EC925605745E409F14BB6C570FF59ACA" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="7cde7a72-9a6b-4ed9-a809-79ca20bf45b4" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4a26497a6ddfc9a61e9c0e463e4c246c5d734f80" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -22,19 +22,18 @@
  </referenceableParamGroup>
  <referenceableParamGroup id="scan1">
  <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="mzArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  </referenceableParamGroupList>
  <sampleList count="1">
@@ -43,18 +42,24 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="1.12.1">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
  <scanSettingsList count="1">
  <scanSettings id="scansettings1">
  <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
- <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" />
+ <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="1" />
+ <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="2" />
+ <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
+ <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="Inf" />
  </scanSettings>
  </scanSettingsList>
  <instrumentConfigurationList count="1">
- <instrumentConfiguration id="IC1" />
+ <instrumentConfiguration id="IC1">
+ <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+ </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="1">
  <dataProcessing id="CardinalWriteImzML">
@@ -73,6 +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="2" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -100,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -127,6 +136,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out3.imzml.txt
--- a/test-data/out3.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out3.imzml.txt Wed Mar 25 05:31:15 2020 -0400
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@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli 9616 Feb 12 19:18 ibd
--rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml
+-rw-r--r-- 1 meli meli 9616 Mär 24 20:25 ibd
+-rw-r--r-- 1 meli meli 8958 Mär 24 20:25 imzml
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out4.ibd
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out4.imzml
--- a/test-data/out4.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out4.imzml Wed Mar 25 05:31:15 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{2567A8C4-D2AF-4C81-874C-82E9134A080C}" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="EA722C9CF5A229ACF6AEAD177908D73A1C8CB44E" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="b0dec95e-b66f-4c3f-86df-166d942f42c3" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d9b557cf2c0e15a0cdd863e50897b07a55a26f31" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -22,19 +22,18 @@
  </referenceableParamGroup>
  <referenceableParamGroup id="scan1">
  <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="mzArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  </referenceableParamGroupList>
  <sampleList count="1">
@@ -43,18 +42,24 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="1.12.1">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
  <scanSettingsList count="1">
  <scanSettings id="scansettings1">
- <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="2.000000" />
+ <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
  </scanSettings>
  </scanSettingsList>
  <instrumentConfigurationList count="1">
- <instrumentConfiguration id="IC1" />
+ <instrumentConfiguration id="IC1">
+ <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+ </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="1">
  <dataProcessing id="CardinalWriteImzML">
@@ -73,6 +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">
@@ -100,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -127,6 +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="2" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -154,6 +165,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -181,6 +194,8 @@
  <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">
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out4.imzml.txt
--- a/test-data/out4.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out4.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 44
--rw-r--r-- 1 meli meli 28792 Feb 12 00:49 ibd
--rw-r--r-- 1 meli meli 11141 Feb 12 00:49 imzml
+-rw-r--r-- 1 meli meli 28792 Mär 24 19:23 ibd
+-rw-r--r-- 1 meli meli 12046 Mär 24 19:23 imzml
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out5.ibd
b
Binary file test-data/out5.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out5.imzml
--- a/test-data/out5.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out5.imzml Wed Mar 25 05:31:15 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{CC0B2B92-FB40-42C8-822F-834AA528954C}" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0B644915E88274BE83FBB110D4CC6D0CDFABAAAC" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="87b0ab73-abe6-4eb6-91ba-b6d493a343bc" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9de3a02d0943ecda0717845511a8f7b8f58d1db7" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -22,19 +22,18 @@
  </referenceableParamGroup>
  <referenceableParamGroup id="scan1">
  <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="mzArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  </referenceableParamGroupList>
  <sampleList count="1">
@@ -43,18 +42,24 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="1.12.1">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
  <scanSettingsList count="1">
  <scanSettings id="scansettings1">
  <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
- <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" />
+ <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
+ <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
  </scanSettings>
  </scanSettingsList>
  <instrumentConfigurationList count="1">
- <instrumentConfiguration id="IC1" />
+ <instrumentConfiguration id="IC1">
+ <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+ </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="1">
  <dataProcessing id="CardinalWriteImzML">
@@ -73,6 +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="2" />
+ <userParam name="3DPositionX" value="1.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -100,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -127,6 +136,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -154,6 +165,8 @@
  <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">
@@ -181,6 +194,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -208,6 +223,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out5.imzml.txt
--- a/test-data/out5.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out5.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 20
--rw-r--r-- 1 meli meli   380 Feb 12 00:50 ibd
--rw-r--r-- 1 meli meli 12508 Feb 12 00:50 imzml
+-rw-r--r-- 1 meli meli   380 Mär 24 19:24 ibd
+-rw-r--r-- 1 meli meli 13525 Mär 24 19:24 imzml
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out6.ibd
b
Binary file test-data/out6.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out6.imzml
--- a/test-data/out6.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out6.imzml Wed Mar 25 05:31:15 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{24BF18EC-E1DE-4B67-BC12-C3EB475CFC0A}" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="DA0417F6AA4EDD71F808B6EA0D7A0706737464EB" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="8b625a26-987e-4e32-b7d4-729efe840814" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="78e6eb56507d789575ee0495e60f9d44a192c0dd" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -22,19 +22,18 @@
  </referenceableParamGroup>
  <referenceableParamGroup id="scan1">
  <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="mzArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  </referenceableParamGroupList>
  <sampleList count="1">
@@ -43,7 +42,7 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="1.12.1">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
@@ -51,10 +50,16 @@
  <scanSettings id="scansettings1">
  <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
+ <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
  </scanSettings>
  </scanSettingsList>
  <instrumentConfigurationList count="1">
- <instrumentConfiguration id="IC1" />
+ <instrumentConfiguration id="IC1">
+ <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+ </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="1">
  <dataProcessing id="CardinalWriteImzML">
@@ -73,6 +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">
@@ -100,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -127,6 +136,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -154,6 +165,8 @@
  <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">
@@ -181,6 +194,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -208,6 +223,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -235,6 +252,8 @@
  <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">
@@ -262,6 +281,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -289,6 +310,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out6.imzml.txt
--- a/test-data/out6.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out6.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 164
--rw-r--r-- 1 meli meli 146896 Feb 12 00:51 ibd
--rw-r--r-- 1 meli meli  16868 Feb 12 00:51 imzml
+-rw-r--r-- 1 meli meli 146896 Mär 24 19:25 ibd
+-rw-r--r-- 1 meli meli  18221 Mär 24 19:25 imzml
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out7.ibd
b
Binary file test-data/out7.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out7.imzml
--- a/test-data/out7.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out7.imzml Wed Mar 25 05:31:15 2020 -0400
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{B095BB77-684D-4BFF-82D3-B76D0EB1C0CD}" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="628A551B81DCF301B65E3A5AB1182F0BF319533C" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="bf61653e-aa1a-4f9a-a84d-3ff3435ee7fe" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="352c33defde6728b7dfb83e18ed1c433fa4b8697" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -22,19 +22,18 @@
  </referenceableParamGroup>
  <referenceableParamGroup id="scan1">
  <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="mzArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  </referenceableParamGroupList>
  <sampleList count="1">
@@ -43,7 +42,7 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="1.12.1">
+ <software id="Cardinal" version="2.4.0">
  <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
  </software>
  </softwareList>
@@ -51,10 +50,16 @@
  <scanSettings id="scansettings1">
  <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
+ <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
  </scanSettings>
  </scanSettingsList>
  <instrumentConfigurationList count="1">
- <instrumentConfiguration id="IC1" />
+ <instrumentConfiguration id="IC1">
+ <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+ </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="1">
  <dataProcessing id="CardinalWriteImzML">
@@ -73,6 +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">
@@ -100,6 +107,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -127,6 +136,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="1.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -154,6 +165,8 @@
  <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">
@@ -181,6 +194,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -208,6 +223,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="2.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -235,6 +252,8 @@
  <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">
@@ -262,6 +281,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="2.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
@@ -289,6 +310,8 @@
  <referenceableParamGroupRef ref="scan1" />
  <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />
  <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />
+ <userParam name="3DPositionX" value="3.000000" />
+ <userParam name="3DPositionY" value="3.000000" />
  </scan>
  </scanList>
  <binaryDataArrayList count="2">
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out7.imzml.txt
--- a/test-data/out7.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/out7.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 116
--rw-r--r-- 1 meli meli 95976 Feb 12 00:51 ibd
--rw-r--r-- 1 meli meli 16846 Feb 12 00:51 imzml
+-rw-r--r-- 1 meli meli 95976 Mär 24 19:26 ibd
+-rw-r--r-- 1 meli meli 18199 Mär 24 19:26 imzml
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out8.ibd
b
Binary file test-data/out8.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out8.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out8.imzml Wed Mar 25 05:31:15 2020 -0400
b
b'@@ -0,0 +1,224 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="ace74b18-25e2-4722-89f4-6eedc2b62ed8" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="41d580d8acf3e67df8b63f001fe941da7334861b" />\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+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="2.4.0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000401" name="top down" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="2" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="2.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" na'..b'/>\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=4" defaultArrayLength="0" index="4">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="3.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="2.000000" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\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="201592" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=5" defaultArrayLength="0" index="5">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="1.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\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="268784" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out8.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out8.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -0,0 +1,4 @@
+imzML file:
+total 348
+-rw-r--r-- 1 meli meli 335976 Mär 24 19:27 ibd
+-rw-r--r-- 1 meli meli  12402 Mär 24 19:27 imzml
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results1.ibd
b
Binary file test-data/preprocessing_results1.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results1.imzml
--- a/test-data/preprocessing_results1.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/preprocessing_results1.imzml Wed Mar 25 05:31:15 2020 -0400
b
b'@@ -9,8 +9,8 @@\n \t\t<fileContent>\n \t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{728FBFFE-E6FC-4283-8068-393A66F6BD5C}" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="375094460F3B80674CB2F541DCD9928B3D61B2FF" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="722d404b-4188-40b4-a3b2-3764ebbdecad" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c5aded0bab57fd7317901ff7709f2395fc91152e" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -22,19 +22,18 @@\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="scan1">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="mzArray">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="intensityArray">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n \t\t</referenceableParamGroup>\n \t</referenceableParamGroupList>\n \t<sampleList count="1">\n@@ -43,7 +42,7 @@\n \t\t</sample>\n \t</sampleList>\n \t<softwareList count="1">\n-\t\t<software id="Cardinal" version="1.12.1">\n+\t\t<software id="Cardinal" version="2.4.0">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n \t\t</software>\n \t</softwareList>\n@@ -51,10 +50,16 @@\n \t\t<scanSettings id="scansettings1">\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />\n \t\t</scanSettings>\n \t</scanSettingsList>\n \t<instrumentConfigurationList count="1">\n-\t\t<instrumentConfiguration id="IC1" />\n+\t\t<instrumentConfiguration id="IC1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t</instrumentConfiguration>\n \t</instrumentConfigurationList>\n \t<dataProcessingList count="1">\n \t\t<dataProcessing id="CardinalWriteImzML">\n@@ -73,21 +78,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="1.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referencea'..b'ernal array length" value="2" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="156" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -262,21 +281,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="2.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="176" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -289,21 +310,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="3.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="88" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="2" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="196" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n'
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results1.imzml.txt
--- a/test-data/preprocessing_results1.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/preprocessing_results1.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-r--r-- 1 meli meli    96 Feb 24 14:11 ibd
--rw-r--r-- 1 meli meli 16714 Feb 24 14:11 imzml
+-rw-r--r-- 1 meli meli   216 Mär 24 10:39 ibd
+-rw-r--r-- 1 meli meli 18090 Mär 24 10:39 imzml
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results1.pdf
b
Binary file test-data/preprocessing_results1.pdf has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results2.ibd
b
Binary file test-data/preprocessing_results2.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results2.imzml
--- a/test-data/preprocessing_results2.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/preprocessing_results2.imzml Wed Mar 25 05:31:15 2020 -0400
b
b'@@ -9,8 +9,8 @@\n \t\t<fileContent>\n \t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{40F230A1-1893-4A8C-BAE2-A8BBEF24DB20}" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="417ADF38FBC4D0304A9B75B4C85799137846DD2F" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="e536d1e2-427b-4c5b-9743-8210ae52a564" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7cea783e9d345946b874fc1f25d40ce90bffd2f9" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -22,19 +22,18 @@\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="scan1">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="mzArray">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="intensityArray">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n \t\t</referenceableParamGroup>\n \t</referenceableParamGroupList>\n \t<sampleList count="1">\n@@ -43,18 +42,24 @@\n \t\t</sample>\n \t</sampleList>\n \t<softwareList count="1">\n-\t\t<software id="Cardinal" version="1.12.1">\n+\t\t<software id="Cardinal" version="2.4.0">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n \t\t</software>\n \t</softwareList>\n \t<scanSettingsList count="1">\n \t\t<scanSettings id="scansettings1">\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="9" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="4" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="9" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />\n \t\t</scanSettings>\n \t</scanSettingsList>\n \t<instrumentConfigurationList count="1">\n-\t\t<instrumentConfiguration id="IC1" />\n+\t\t<instrumentConfiguration id="IC1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t</instrumentConfiguration>\n \t</instrumentConfigurationList>\n \t<dataProcessingList count="1">\n \t\t<dataProcessing id="CardinalWriteImzML">\n@@ -73,21 +78,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="1.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scan'..b'" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="28776" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -343,21 +368,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="9.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="2.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="46304" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="31652" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -370,21 +397,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="9.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="50512" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="34528" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n'
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results2.imzml.txt
--- a/test-data/preprocessing_results2.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/preprocessing_results2.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
-total 80
--rw-r--r-- 1 meli meli 54720 Feb 24 14:12 ibd
--rw-r--r-- 1 meli meli 21132 Feb 24 14:12 imzml
+total 64
+-rw-r--r-- 1 meli meli 37404 Mär 24 10:40 ibd
+-rw-r--r-- 1 meli meli 22796 Mär 24 10:40 imzml
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results2.pdf
b
Binary file test-data/preprocessing_results2.pdf has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results3.ibd
b
Binary file test-data/preprocessing_results3.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results3.imzml
--- a/test-data/preprocessing_results3.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/preprocessing_results3.imzml Wed Mar 25 05:31:15 2020 -0400
b
b'@@ -9,8 +9,8 @@\n \t\t<fileContent>\n \t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{D767424F-5E74-45AB-AF1B-0D25244B435B}" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="445E32981D0B3D08ED2BA74E11500A3A08CDB9B7" />\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</fileContent>\n \t</fileDescription>\n@@ -22,19 +22,18 @@\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="scan1">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="mzArray">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="intensityArray">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n \t\t</referenceableParamGroup>\n \t</referenceableParamGroupList>\n \t<sampleList count="1">\n@@ -43,7 +42,7 @@\n \t\t</sample>\n \t</sampleList>\n \t<softwareList count="1">\n-\t\t<software id="Cardinal" version="1.12.1">\n+\t\t<software id="Cardinal" version="2.4.0">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n \t\t</software>\n \t</softwareList>\n@@ -51,10 +50,16 @@\n \t\t<scanSettings id="scansettings1">\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />\n \t\t</scanSettings>\n \t</scanSettingsList>\n \t<instrumentConfigurationList count="1">\n-\t\t<instrumentConfiguration id="IC1" />\n+\t\t<instrumentConfiguration id="IC1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t</instrumentConfiguration>\n \t</instrumentConfigurationList>\n \t<dataProcessingList count="1">\n \t\t<dataProcessing id="CardinalWriteImzML">\n@@ -73,21 +78,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="1.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referencea'..b' />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -262,21 +281,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="2.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<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<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="11376" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="112" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -289,21 +310,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="3.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<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<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="12796" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="355" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1420" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="124" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="12" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n'
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results3.imzml.txt
--- a/test-data/preprocessing_results3.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/preprocessing_results3.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
-total 36
--rw-r--r-- 1 meli meli 14216 Feb 24 14:12 ibd
--rw-r--r-- 1 meli meli 16824 Feb 24 14:12 imzml
+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
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results3.pdf
b
Binary file test-data/preprocessing_results3.pdf has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results4.ibd
b
Binary file test-data/preprocessing_results4.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results4.imzml
--- a/test-data/preprocessing_results4.imzml Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/preprocessing_results4.imzml Wed Mar 25 05:31:15 2020 -0400
b
b'@@ -9,8 +9,8 @@\n \t\t<fileContent>\n \t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{FE932E04-42E4-4D89-B721-2A6CE83250B6}" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="36C7C916C176DD85CBBF4B7FA969C92B9403768D" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="db79298c-8368-42d7-84fc-18cad6ef1924" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="18bae3cc87b4c9aab2577cffe2fbc7425a93270b" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -22,19 +22,18 @@\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="scan1">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="mzArray">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="intensityArray">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n \t\t</referenceableParamGroup>\n \t</referenceableParamGroupList>\n \t<sampleList count="1">\n@@ -43,7 +42,7 @@\n \t\t</sample>\n \t</sampleList>\n \t<softwareList count="1">\n-\t\t<software id="Cardinal" version="1.12.1">\n+\t\t<software id="Cardinal" version="2.4.0">\n \t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n \t\t</software>\n \t</softwareList>\n@@ -51,10 +50,16 @@\n \t\t<scanSettings id="scansettings1">\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />\n \t\t</scanSettings>\n \t</scanSettingsList>\n \t<instrumentConfigurationList count="1">\n-\t\t<instrumentConfiguration id="IC1" />\n+\t\t<instrumentConfiguration id="IC1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t</instrumentConfiguration>\n \t</instrumentConfigurationList>\n \t<dataProcessingList count="1">\n \t\t<dataProcessing id="CardinalWriteImzML">\n@@ -73,21 +78,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="1.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="1.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceab'..b'f="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="44284" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -262,21 +281,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="2.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="5104" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="50608" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -289,21 +310,23 @@\n \t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="3.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n \t\t\t\t\t</scan>\n \t\t\t\t</scanList>\n \t\t\t\t<binaryDataArrayList count="2">\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="5740" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="159" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="636" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="56932" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1581" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="6324" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n'
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results4.imzml.txt
--- a/test-data/preprocessing_results4.imzml.txt Fri Dec 13 13:51:29 2019 -0500
+++ b/test-data/preprocessing_results4.imzml.txt Wed Mar 25 05:31:15 2020 -0400
b
@@ -1,4 +1,4 @@
 imzML file:
-total 28
--rw-r--r-- 1 meli meli  6376 Feb 24 14:13 ibd
--rw-r--r-- 1 meli meli 16801 Feb 24 14:13 imzml
+total 84
+-rw-r--r-- 1 meli meli 63256 Mär 24 11:35 ibd
+-rw-r--r-- 1 meli meli 18199 Mär 24 11:35 imzml
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results4.pdf
b
Binary file test-data/preprocessing_results4.pdf has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results5.RData
b
Binary file test-data/preprocessing_results5.RData has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results5.ibd
b
Binary file test-data/preprocessing_results5.ibd has changed
b
diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results5.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results5.imzml Wed Mar 25 05:31:15 2020 -0400
b
b'@@ -0,0 +1,340 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c88c7d70-c027-4fa3-b274-0af5e7f4d117" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="16a0f87989392c55b1c02770f15095dcf0d9408e" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="2.4.0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000401" name="top down" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" n'..b'rray" />\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="10398" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41592" />\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="291160" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10398" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41592" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="2.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\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="10398" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41592" />\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="332752" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10398" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41592" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="3.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\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="10398" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41592" />\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="374344" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10398" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41592" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results5.imzml.txt
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+++ b/test-data/preprocessing_results5.imzml.txt Wed Mar 25 05:31:15 2020 -0400
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@@ -0,0 +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
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results5.pdf
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diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/rdata_notfiltered.pdf
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