Mercurial > repos > galaxyp > cardinal_combine

changeset 10:d64858cd48c6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 888b3e991d0752b694bf480531ce0e5318c2f337-dirty"
author galaxyp
date Fri, 07 May 2021 09:50:35 +0000
parents 11d9b3ebbabd
children 268f8b213cee
files combine.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/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_imzml.pdf test-data/Plot_picked.pdf test-data/Plot_processed.pdf test-data/Plot_rdata.pdf test-data/centroids_proc.pdf test-data/pixels_test6.tabular 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/test6.pdf test-data/test6.rdata
diffstat 28 files changed, 142 insertions(+), 137 deletions(-) [+]
line wrap: on
line diff
--- a/combine.xml	Tue Nov 03 22:22:18 2020 +0000
+++ b/combine.xml	Fri May 07 09:50:35 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0">
+<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1">
     <description>
         combine several mass spectrometry imaging datasets into one
     </description>
@@ -120,6 +120,11 @@
     ## same name for MSI data files necessary to combine data into one single coordinate system
     run(msidata_$i) = "msidata"
 
+    ## remove z dimension and 3D information in pixelData to allow combining datasets with and without z dimension
+    coord(msidata_${i})\$z <- NULL
+    pData(msidata_${i})\$'3DPositionX' <- NULL
+    pData(msidata_${i})\$'3DPositionY' <- NULL
+
 ############ 3) Read and process annotation tabular files ######################
 
     #if str($annotation_cond.annotation_tabular) == 'annotation'
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/Plot_analyze75.pdf has changed
Binary file test-data/Plot_analyze75_allpixels.pdf has changed
Binary file test-data/Plot_imzml.pdf has changed
Binary file test-data/Plot_picked.pdf has changed
Binary file test-data/Plot_processed.pdf has changed
Binary file test-data/Plot_rdata.pdf has changed
Binary file test-data/centroids_proc.pdf has changed
--- a/test-data/pixels_test6.tabular	Tue Nov 03 22:22:18 2020 +0000
+++ b/test-data/pixels_test6.tabular	Fri May 07 09:50:35 2021 +0000
@@ -1,25 +1,25 @@
-pixel names	x	y	predicted condition
-xy_1_1	1	1	A
-xy_2_1	2	1	A
-xy_3_1	3	1	B
-xy_4_1	4	1	C
-xy_1_2	1	2	C
-xy_2_2	2	2	C
-xy_3_2	3	2	A
-xy_4_2	4	2	A
-xy_1_3	1	3	A
-xy_2_3	2	3	B
-xy_3_3	3	3	C
-xy_4_3	4	3	A
-xy_10_1	10	1	C
-xy_11_1	11	1	C
-xy_12_1	12	1	C
-xy_13_1	13	1	B
-xy_10_2	10	2	C
-xy_11_2	11	2	B
-xy_12_2	12	2	C
-xy_13_2	13	2	C
-xy_10_3	10	3	C
-xy_11_3	11	3	C
-xy_12_3	12	3	B
-xy_13_3	13	3	C
+pixel names	x	y	predicted condition	A	B	C
+xy_1_1	1	1	A	0.434439526064797	0.195646317191818	0.369914156743386
+xy_2_1	2	1	A	0.38219998209377	0.242372158141275	0.375427859764956
+xy_3_1	3	1	B	0.312531499299517	0.385612104162858	0.301856396537625
+xy_4_1	4	1	C	0.393153488582866	0.191107087820634	0.4157394235965
+xy_1_2	1	2	C	0.366986470447772	0.216121568441093	0.416891961111135
+xy_2_2	2	2	C	0.381682206547616	0.213188918797062	0.405128874655322
+xy_3_2	3	2	A	0.376695037169723	0.260689491088564	0.362615471741713
+xy_4_2	4	2	A	0.42305935188829	0.174038449100755	0.402902199010954
+xy_1_3	1	3	A	0.382420991383021	0.249364697048677	0.368214311568302
+xy_2_3	2	3	B	0.272145998315727	0.446525938567718	0.281328063116555
+xy_3_3	3	3	C	0.36296987427851	0.255631013944556	0.381399111776934
+xy_4_3	4	3	A	0.444812272103175	0.132274264153212	0.422913463743613
+xy_10_1	10	1	C	0.376216993893763	0.227584528606788	0.39619847749945
+xy_11_1	11	1	C	0.358430578177403	0.236120068794936	0.405449353027661
+xy_12_1	12	1	C	0.359751662628136	0.218620985552221	0.421627351819643
+xy_13_1	13	1	B	0.101486342705225	0.813997511218961	0.0845161460758142
+xy_10_2	10	2	C	0.354612526523361	0.272635192773437	0.372752280703202
+xy_11_2	11	2	B	0.291635599769993	0.444466545540823	0.263897854689184
+xy_12_2	12	2	C	0.36763798979782	0.203911653614431	0.428450356587749
+xy_13_2	13	2	C	0.344608135177236	0.304026642707691	0.351365222115073
+xy_10_3	10	3	C	0.37046458150651	0.205561286708086	0.423974131785404
+xy_11_3	11	3	C	0.358113833435286	0.262878459144526	0.379007707420187
+xy_12_3	12	3	B	0.180921926305915	0.66902588624642	0.150052187447665
+xy_13_3	13	3	C	0.378266307042675	0.20859472985319	0.413138963104135
Binary file test-data/preprocessing_results1.ibd has changed
--- a/test-data/preprocessing_results1.imzml	Tue Nov 03 22:22:18 2020 +0000
+++ b/test-data/preprocessing_results1.imzml	Fri May 07 09:50:35 2021 +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	Tue Nov 03 22:22:18 2020 +0000
+++ b/test-data/preprocessing_results1.imzml.txt	Fri May 07 09:50:35 2021 +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	Tue Nov 03 22:22:18 2020 +0000
+++ b/test-data/preprocessing_results2.imzml	Fri May 07 09:50:35 2021 +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	Tue Nov 03 22:22:18 2020 +0000
+++ b/test-data/preprocessing_results2.imzml.txt	Fri May 07 09:50:35 2021 +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	Tue Nov 03 22:22:18 2020 +0000
+++ b/test-data/preprocessing_results3.imzml	Fri May 07 09:50:35 2021 +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" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4ee7ca6fb3f60e1adbe196068f86bc3209bace58" />
-			<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="476b127d-a8e1-4595-aae9-e9245db50d28" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="8a36ea2658fcfc8cfa9ae4d0dd73cd7ed2f5b96f" />
+			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
 	<referenceableParamGroupList count="4">
@@ -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="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="64" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="16" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="64" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="160" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -114,16 +114,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="144" />
-						<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="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="164" />
-						<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="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -143,16 +143,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="184" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="18" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="256" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="18" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="448" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -172,16 +172,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="328" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="21" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="84" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="412" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="21" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="84" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="592" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -201,16 +201,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="496" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="4" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="512" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="4" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="736" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -230,16 +230,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="528" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="18" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="600" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="18" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="72" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="880" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -259,16 +259,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="672" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="68" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="740" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="68" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1024" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -288,16 +288,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="808" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="840" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1168" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -317,16 +317,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="872" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="11" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="44" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="916" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="11" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="44" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1312" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
--- a/test-data/preprocessing_results3.imzml.txt	Tue Nov 03 22:22:18 2020 +0000
+++ b/test-data/preprocessing_results3.imzml.txt	Fri May 07 09:50:35 2021 +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
Binary file test-data/test6.pdf has changed
Binary file test-data/test6.rdata has changed