Mercurial > repos > galaxyp > cardinal_mz_images

changeset 13:a2b57ea6666e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"
author galaxyp
date Sun, 29 Nov 2020 23:23:01 +0000
parents a95a82eb4d50
children 59e85306eae5
files mz_images.xml test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_processed.pdf test-data/Heatmaps_rdata.pdf test-data/centroids_proc.pdf 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
diffstat 19 files changed, 135 insertions(+), 118 deletions(-) [+]
line wrap: on
line diff
--- a/mz_images.xml	Wed Oct 21 22:58:11 2020 +0000
+++ b/mz_images.xml	Sun Nov 29 23:23:01 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.1">
+<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.2">
     <description>
         mass spectrometry imaging m/z heatmaps
     </description>
@@ -62,12 +62,19 @@
 
 ### only plot images when file has features and pixels: 
 par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
+
+#if str($light_mode) == "white":
+    lightmode()
+#else
+    darkmode()
+#end if
+
 if (ncol(msidata)>0 & nrow(msidata) >0){
     if (length(inputmz) != 0){
         for (mass in 1:length(inputmz)){
 
                 print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", 
-                smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))
+                smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, alpha.power=$alpha_power, ylim= c(maximumy,minimumy)))
                 title(inputnames[mass], adj = 0.5, line = 1)}
 
 
@@ -81,7 +88,12 @@
 
             svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
             par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg
-            print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton, colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", normalize.image="$normalize_image"))
+	    #if str($light_mode) == "white":
+	        lightmode()
+	    #else
+	        darkmode()
+	    #end if
+            print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", alpha.power=$alpha_power, normalize.image="$normalize_image"))
             dev.off()
         #end if
 
@@ -90,15 +102,14 @@
 
         #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours])
         colourvector = c($color_string)
-            par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
             print(image(msidata, mz=inputmz, 
                   plusminus = $plusminus_dalton,
-                  col=colourvector,
+                  col=colourvector, 
                   contrast.enhance = "$image_contrast", 
                   normalize.image="$normalize_image", 
                   smooth.image = "$image_smoothing",
                   superpose=TRUE, main="overlay of all m/z", 
-                  key=FALSE, 
+                  key=FALSE, alpha.power=$alpha_power,
                   ylim= c(maximumy,minimumy)))
 
              legend("$overlay_cond.legend_position",
@@ -121,7 +132,7 @@
         <expand macro="pdf_filename"/>
         <expand macro="reading_2_column_mz_tabular"/>
 
-        <param name="plusminus_dalton" value="0.25" type="float" label="m/z range" help="average of the m/z window will be computed"/>
+        <param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/>
         <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
             <option value="none" selected="True">none</option>
             <option value="suppression">suppression</option>
@@ -138,6 +149,11 @@
             <option value="plasma">plasma</option>
             <option value="inferno">inferno</option>
         </param>
+        <param name="light_mode" type="select" display="radio" label="Image Background">
+            <option value="white" selected="True">white</option>
+            <option value="black">black</option>
+        </param>
+        <param name="alpha_power" type="float" value="1" label="Alpha power" help="Opacity scaling factor (1 is linear)"/>
         <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
         <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/>
         <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
@@ -233,6 +249,7 @@
             <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
             <param name="mz_column" value="1"/>
             <param name="name_column" value="2"/>
+            <param name="light_mode" value="black"/>
             <conditional name="overlay_cond">
                 <param name="overlay_selection" value="yes_overlay"/>
                 <repeat name="colours">
Binary file test-data/Heatmaps_LM8_file16.pdf has changed
Binary file test-data/Heatmaps_analyze75.pdf has changed
Binary file test-data/Heatmaps_imzml.pdf has changed
Binary file test-data/Heatmaps_processed.pdf has changed
Binary file test-data/Heatmaps_rdata.pdf has changed
Binary file test-data/centroids_proc.pdf has changed
Binary file test-data/preprocessing_results1.ibd has changed
--- a/test-data/preprocessing_results1.imzml	Wed Oct 21 22:58:11 2020 +0000
+++ b/test-data/preprocessing_results1.imzml	Sun Nov 29 23:23:01 2020 +0000
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="07177fdd-3760-4df6-8fe2-53d28b280ae8" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="749fe32c8243da06001cf4643c5ce4f1ef5a98a8" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="22bd3147-231d-4076-b6bd-67c1fa7c6ef3" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="831eba0fc850529d1351bcbb1baf779fe0773e1b" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
@@ -86,15 +86,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="36" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="48" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -115,15 +115,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="56" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -144,15 +144,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="76" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="112" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -173,15 +173,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="96" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="144" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -202,15 +202,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="116" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="176" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -231,15 +231,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="136" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="208" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -260,15 +260,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="156" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="240" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -289,15 +289,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="176" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="272" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -318,15 +318,15 @@
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
 						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="196" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="304" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
--- a/test-data/preprocessing_results1.imzml.txt	Wed Oct 21 22:58:11 2020 +0000
+++ b/test-data/preprocessing_results1.imzml.txt	Sun Nov 29 23:23:01 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-rw-r-- 1 meli meli   216 Oct  5 19:57 ibd
--rw-rw-r-- 1 meli meli 18090 Oct  5 19:57 imzml
+-rw-rw-r-- 1 meli meli   336 Nov 29 01:14 ibd
+-rw-rw-r-- 1 meli meli 18092 Nov 29 01:14 imzml
Binary file test-data/preprocessing_results1.pdf has changed
Binary file test-data/preprocessing_results2.ibd has changed
--- a/test-data/preprocessing_results2.imzml	Wed Oct 21 22:58:11 2020 +0000
+++ b/test-data/preprocessing_results2.imzml	Sun Nov 29 23:23:01 2020 +0000
@@ -9,8 +9,8 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="503079b4-538a-4be6-b70d-e52542c66482" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a597fe6a0184ef339105b3a932f58726a9af549b" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="ebbd9c5a-19a7-4db5-91e0-858065743606" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="471a838ffd01331ad8e6d23a59004e05745bf39c" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/preprocessing_results2.imzml.txt	Wed Oct 21 22:58:11 2020 +0000
+++ b/test-data/preprocessing_results2.imzml.txt	Sun Nov 29 23:23:01 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 64
--rw-rw-r-- 1 meli meli 37404 Oct  5 19:57 ibd
--rw-rw-r-- 1 meli meli 22796 Oct  5 19:57 imzml
+-rw-rw-r-- 1 meli meli 37404 Nov 29 18:03 ibd
+-rw-rw-r-- 1 meli meli 22796 Nov 29 18:03 imzml
Binary file test-data/preprocessing_results2.pdf has changed
Binary file test-data/preprocessing_results3.ibd has changed
--- a/test-data/preprocessing_results3.imzml	Wed Oct 21 22:58:11 2020 +0000
+++ b/test-data/preprocessing_results3.imzml	Sun Nov 29 23:23:01 2020 +0000
@@ -9,9 +9,9 @@
 		<fileContent>
 			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
 			<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
-			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="be549a7e-87af-4413-9b4c-27221f55ee9a" />
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-			<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="64" />
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@@ -114,16 +114,16 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="84" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16" />
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+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16" />
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@@ -230,16 +230,16 @@
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+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="880" />
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@@ -259,16 +259,16 @@
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@@ -288,16 +288,16 @@
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
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-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="44" />
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--- a/test-data/preprocessing_results3.imzml.txt	Wed Oct 21 22:58:11 2020 +0000
+++ b/test-data/preprocessing_results3.imzml.txt	Sun Nov 29 23:23:01 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-rw-r-- 1 meli meli   960 Oct  5 19:58 ibd
--rw-rw-r-- 1 meli meli 18112 Oct  5 19:58 imzml
+-rw-rw-r-- 1 meli meli  1456 Nov 29 18:04 ibd
+-rw-rw-r-- 1 meli meli 18133 Nov 29 18:04 imzml
Binary file test-data/preprocessing_results3.pdf has changed