Mercurial > repos > galaxyp > cardinal_preprocessing

changeset 10:5abc3ab4792c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a"
author galaxyp
date Sun, 27 Sep 2020 11:10:30 +0000
parents ca727a6dede6
children e86a8be551b9
files macros.xml preprocessing.xml test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75_filtered2.pdf test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/imzml_filtered8.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/out8.ibd test-data/out8.imzml test-data/out8.imzml.txt test-data/rdata_notfiltered.pdf
diffstat 30 files changed, 84 insertions(+), 98 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Sep 24 11:43:31 2020 +0000
+++ b/macros.xml	Sun Sep 27 11:10:30 2020 +0000
@@ -117,6 +117,13 @@
     <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ 
 ########################### QC numbers ########################
 ## including intensity calculations which need data in RAM
+
+	int_matrix = as.matrix(spectra(msidata)) ## only load once into RAM, then re-use
+	## Number of NA in spectra matrix
+        NAcount = sum(is.na(int_matrix))
+	## replace NA with zero to calculate data properties based on intensity matrix, no change in msidata
+	int_matrix[is.na(int_matrix)] <- 0
+	
         ## Number of features (mz)
         maxfeatures = length(features(msidata))
         ## Range mz
@@ -131,14 +138,12 @@
         minimumy = min(coord(msidata)[,2])
         maximumy = max(coord(msidata)[,2])
         ## Range of intensities
-        minint = round(min(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
-        maxint = round(max(as.matrix(spectra(msidata)), na.rm=TRUE), digits=2)
+        minint = round(min(int_matrix), digits=2)
+        maxint = round(max(int_matrix), digits=2)
         ## Number of intensities > 0, for if conditions
-        npeaks= sum(as.matrix(spectra(msidata))>0, na.rm=TRUE)
+        npeaks= sum(int_matrix>0)
         ## Number of NA in spectra matrix
-        NAcount = sum(is.na(spectra(msidata)))
-        ## Number of NA in spectra matrix
-        infcount = sum(is.infinite(as.matrix(spectra(msidata))))
+        infcount = sum(is.infinite(int_matrix))
         ## Number of duplicated coordinates
         dupl_coord = sum(duplicated(coord(msidata)))
         properties = c("Number of m/z features",
--- a/preprocessing.xml	Thu Sep 24 11:43:31 2020 +0000
+++ b/preprocessing.xml	Sun Sep 27 11:10:30 2020 +0000
@@ -74,7 +74,7 @@
     ## Choose random spectra for QC plots
     random_spectra = sample(pixels(msidata), 4, replace=FALSE)
     par(oma=c(0,0,2,0))
-    print(plot(msidata, pixel=random_spectra))
+    print(plot(msidata, pixel=random_spectra, col="black"))
     title("Input spectra", outer=TRUE, line=0)
 
     ############################### Preprocessing steps ###########################
@@ -88,10 +88,6 @@
             print('Normalization')
             ##normalization
 
-            if (class(msidata) == "MSProcessedImagingExperiment"){
-                msidata = as(msidata, "MSContinuousImagingExperiment")
-            }
-
             msidata = normalize(msidata, method="$method.methods_conditional.methods_for_normalization.normalization_method")
             msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
 
@@ -105,7 +101,7 @@
             normalized = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, normalized)
             vectorofactions = append(vectorofactions, "normalized")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after normalization", outer=TRUE, line=0)
 
     ############################### Baseline reduction ###########################
@@ -114,10 +110,6 @@
             print('Baseline_reduction')
             ##baseline reduction
 
-            if (class(msidata) == "MSProcessedImagingExperiment"){
-                msidata = as(msidata, "MSContinuousImagingExperiment")
-            }
-
             msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline)
             msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
 
@@ -130,7 +122,7 @@
             baseline = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, baseline)
             vectorofactions = append(vectorofactions, "baseline red.")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after baseline reduction", outer=TRUE, line=0)
 
     ############################### Smoothing ###########################
@@ -139,11 +131,6 @@
             print('Smoothing')
             ## Smoothing
 
-            if (class(msidata) == "MSProcessedImagingExperiment"){
-                msidata = as(msidata, "MSContinuousImagingExperiment")
-            }
-
-
             #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian':
                 print('gaussian smoothing')
 
@@ -176,7 +163,7 @@
             smoothed = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, smoothed)
             vectorofactions = append(vectorofactions, "smoothed")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after smoothing", outer=TRUE, line=0)
 
 
@@ -211,7 +198,7 @@
             mz_aligned = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, mz_aligned)
             vectorofactions = append(vectorofactions, "mz aligned")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after m/z alignment", outer=TRUE, line=0)
 
 
@@ -240,10 +227,6 @@
             #end if
             msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
 
-            #if str($method.methods_conditional.imzml_output) == "cont_format":
-                #set $continuous_format = True
-            #end if
-
 
             ############################### QC ###########################
 
@@ -254,7 +237,7 @@
             picked = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, picked)
             vectorofactions = append(vectorofactions, "picked")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after peak picking", outer=TRUE, line=0)
 
     ############################### Peak alignment ###########################
@@ -285,9 +268,6 @@
 
             msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))
 
-            #if str($method.methods_conditional.imzml_output) == "cont_format":
-                #set $continuous_format = True
-            #end if
 
             ############################### QC ###########################
 
@@ -298,7 +278,7 @@
             aligned = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, aligned)
             vectorofactions = append(vectorofactions, "aligned")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after alignment", outer=TRUE, line=0)
 
     ############################### Peak filtering ###########################
@@ -318,7 +298,7 @@
             filtered = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, filtered)
             vectorofactions = append(vectorofactions, "filtered")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after filtering", outer=TRUE, line=0)
 
     ############################### Peak binning ###########################
@@ -343,7 +323,7 @@
             peak_binned = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, peak_binned)
             vectorofactions = append(vectorofactions, "peak binned")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after peak binning", outer=TRUE, line=0)
 
 
@@ -387,7 +367,7 @@
             reduced = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, reduced)
             vectorofactions = append(vectorofactions, "reduced")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after m/z binning", outer=TRUE, line=0)
 
         ############################### Transformation ###########################
@@ -430,7 +410,7 @@
             transformed = c(minmz, maxmz,maxfeatures, pixelcount)
             QC_numbers= cbind(QC_numbers, transformed)
             vectorofactions = append(vectorofactions, "transformed")
-            print(plot(msidata, pixel=random_spectra))
+            print(plot(msidata, pixel=random_spectra, col="black"))
             title("Spectra after transformation", outer=TRUE, line=0)
 
             #end if
@@ -440,6 +420,10 @@
     ################################################################################
 
     ## save msidata as imzML file, will only work if there is at least 1 m/z left
+    
+    #if str($imzml_output) == "cont_format":
+        #set $continuous_format = True
+    #end if
 
         if (nrow(msidata) > 0){
             ## make sure that coordinates are integers
@@ -578,7 +562,6 @@
                         <when value="mad"/>
                         <when value="simple"/>
                     </conditional>
-                <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>
                 </when>
                 <when value="Peak_alignment">
                     <param name="value_diffalignment" type="float" value="200"
@@ -597,7 +580,6 @@
                             <expand macro="reading_1_column_mz_tabular" label="Tabular file with m/z features to use for alignment. Only the m/z values from the tabular file will be kept."/>
                         </when>
                     </conditional>
-                <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format" help= "Processed imzML works only in MALDIquant tools, not yet in MSI tools (Cardinal)"/>
                 </when>
                 <when value="Peak_filtering">
                     <param name="frequ_filtering" type="float" value="0.01" max="1" min="0" label="Minimum frequency" help="Peaks that occur in the dataset in lesser proportion than this will be dropped (0.01 --> filtering for 1% of spectra)"/>
@@ -661,6 +643,7 @@
                 </when>
             </conditional>
         </repeat>
+        <param name="imzml_output" type="boolean" label="imzML output in processed format" checked="True" truevalue="proc_format" falsevalue="cont_format"/>
     </inputs>
     <outputs>
         <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
@@ -696,13 +679,11 @@
                     <param name="blocks_picking" value="3"/>
                     <param name="window_picking" value="3"/>
                     <param name="SNR_picking_method" value="3"/>
-                    <param name="imzml_output" value="cont_format"/>
                 </conditional>
             </repeat>
             <repeat name="methods">
                 <conditional name="methods_conditional">
                     <param name="preprocessing_method" value="Peak_alignment"/>
-                    <param name="imzml_output" value="cont_format"/>
                 </conditional>
             </repeat>
             <repeat name="methods">
@@ -719,6 +700,7 @@
                         </conditional>
                 </conditional>
             </repeat>
+            <param name="imzml_output" value="cont_format"/>
             <output name="QC_overview" file="preprocessing_results1.pdf" compare="sim_size"/>
             <output name="outfile_imzml" ftype="imzml" file="preprocessing_results1.imzml.txt" compare="sim_size">
                 <extra_files type="file" file="preprocessing_results1.imzml" name="imzml" lines_diff="6"/>
@@ -736,15 +718,14 @@
                     <conditional name="methods_for_picking">
                         <param name="picking_method" value="adaptive"/>
                     </conditional>
-                    <param name="imzml_output" value="cont_format"/>
                 </conditional>
             </repeat>
             <repeat name="methods">
                 <conditional name="methods_conditional">
                     <param name="preprocessing_method" value="Peak_alignment"/>
-                    <param name="imzml_output" value="cont_format"/>
                 </conditional>
             </repeat>
+            <param name="imzml_output" value="cont_format"/>
             <output name="QC_overview" file="preprocessing_results2.pdf" compare="sim_size"/>
             <output name="outfile_imzml" ftype="imzml" file="preprocessing_results2.imzml.txt" compare="sim_size">
                 <extra_files type="file" file="preprocessing_results2.imzml" name="imzml" lines_diff="6"/>
Binary file test-data/QC_analyze75.pdf has changed
Binary file test-data/QC_empty_spectra.pdf has changed
Binary file test-data/QC_imzml.pdf has changed
Binary file test-data/QC_rdata.pdf has changed
Binary file test-data/analyze75_filtered2.pdf has changed
Binary file test-data/imzml_filtered3.pdf has changed
Binary file test-data/imzml_filtered4.pdf has changed
Binary file test-data/imzml_filtered5.pdf has changed
Binary file test-data/imzml_filtered8.pdf has changed
Binary file test-data/out3.ibd has changed
--- a/test-data/out3.imzml	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out3.imzml	Sun Sep 27 11:10:30 2020 +0000
@@ -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="c6cc990a-d910-4c17-aedd-ceb204b4d105" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ef8c4f864d0386736c986ebb4d4eb29a726e42d4" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="97f42eea-750c-49e4-b46d-08c548dc3b9d" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4e046226f81e9c78255df625ca3546ef26dd0693" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/out3.imzml.txt	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out3.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 24
--rw-rw-r-- 1 meli meli 9616 Aug 23 17:39 ibd
--rw-rw-r-- 1 meli meli 8958 Aug 23 17:39 imzml
+-rw-rw-r-- 1 meli meli 9616 Sep 27 10:51 ibd
+-rw-rw-r-- 1 meli meli 8958 Sep 27 10:51 imzml
Binary file test-data/out4.ibd has changed
--- a/test-data/out4.imzml	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out4.imzml	Sun Sep 27 11:10:30 2020 +0000
@@ -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="78fa5a7c-8dc8-4ff1-ad77-b19714f285cb" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="64d40f8c65af1399e24d94569f4dd3fdbf43a901" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="37f3f75a-82c4-47c5-b78e-28fb8697e59b" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1746fd2ec8a12707330a78ff5a0ff98cb53dca42" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/out4.imzml.txt	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out4.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 44
--rw-rw-r-- 1 meli meli 28792 Aug 23 17:39 ibd
--rw-rw-r-- 1 meli meli 12046 Aug 23 17:39 imzml
+-rw-rw-r-- 1 meli meli 28792 Sep 27 10:52 ibd
+-rw-rw-r-- 1 meli meli 12046 Sep 27 10:52 imzml
Binary file test-data/out5.ibd has changed
--- a/test-data/out5.imzml	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out5.imzml	Sun Sep 27 11:10:30 2020 +0000
@@ -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="30751422-deca-429e-9f8e-24639c108d6d" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2c7f19c6447844039a112152c19f7cfd50dbf12e" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="37236c7e-6e93-4ccc-9111-1b1153aac713" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ccb886aaf3cb7564f518884413ea988c59a1de57" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/out5.imzml.txt	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out5.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 20
--rw-rw-r-- 1 meli meli   380 Aug 23 17:40 ibd
--rw-rw-r-- 1 meli meli 13525 Aug 23 17:40 imzml
+-rw-rw-r-- 1 meli meli   380 Sep 27 10:53 ibd
+-rw-rw-r-- 1 meli meli 13525 Sep 27 10:53 imzml
Binary file test-data/out6.ibd has changed
--- a/test-data/out6.imzml	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out6.imzml	Sun Sep 27 11:10:30 2020 +0000
@@ -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="254b991f-92f5-46d5-8069-6f9ecd53b05a" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0aaa784dc2a335da176a4bc2d12a43f2d18bdbf1" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="734d4b50-4440-4747-a0e9-de78974d1487" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b1636b28fd4e0ab9caf5aaa4c1a40760030a4e73" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/out6.imzml.txt	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out6.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 164
--rw-rw-r-- 1 meli meli 146896 Aug 23 17:41 ibd
--rw-rw-r-- 1 meli meli  18221 Aug 23 17:41 imzml
+-rw-rw-r-- 1 meli meli 146896 Sep 27 10:53 ibd
+-rw-rw-r-- 1 meli meli  18221 Sep 27 10:53 imzml
Binary file test-data/out7.ibd has changed
--- a/test-data/out7.imzml	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out7.imzml	Sun Sep 27 11:10:30 2020 +0000
@@ -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="227ecc2e-a494-4018-afc5-45eaa790e812" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="e22162d1dd762607ca6d31c0b8892e0ae5a3a772" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="f81632b3-50b0-4a57-88a2-5f7cf97f9bae" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9f88294c3cff3e8c30e80632d6ad616b7db18089" />
 			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
--- a/test-data/out7.imzml.txt	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out7.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
 total 116
--rw-rw-r-- 1 meli meli 95976 Aug 23 17:41 ibd
--rw-rw-r-- 1 meli meli 18199 Aug 23 17:41 imzml
+-rw-rw-r-- 1 meli meli 95976 Sep 27 10:54 ibd
+-rw-rw-r-- 1 meli meli 18199 Sep 27 10:54 imzml
Binary file test-data/out8.ibd has changed
--- a/test-data/out8.imzml	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out8.imzml	Sun Sep 27 11:10:30 2020 +0000
@@ -9,9 +9,9 @@
 		<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="91ed729b-0b8d-49f6-b832-e4d3834fe733" />
-			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="efd09bddeebeb334efe9dffad3a4f3bed35442d1" />
-			<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />
+			<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="02059ae7-7beb-4ecf-92ae-7a767e04bf43" />
+			<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="dc3960918fa3008824889b4ac142be1d0534ded8" />
+			<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
 		</fileContent>
 	</fileDescription>
 	<referenceableParamGroupList count="4">
@@ -90,15 +90,15 @@
 					<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="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="41484" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -118,16 +118,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="82952" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -147,16 +147,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="124420" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -176,16 +176,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="165888" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
@@ -205,16 +205,16 @@
 				<binaryDataArrayList count="2">
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="mzArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 					<binaryDataArray encodedLength="0">
 						<referenceableParamGroupRef ref="intensityArray" />
-						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380" />
-						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />
-						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="207356" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10367" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="41468" />
 						<binary />
 					</binaryDataArray>
 				</binaryDataArrayList>
--- a/test-data/out8.imzml.txt	Thu Sep 24 11:43:31 2020 +0000
+++ b/test-data/out8.imzml.txt	Sun Sep 27 11:10:30 2020 +0000
@@ -1,4 +1,4 @@
 imzML file:
-total 348
--rw-rw-r-- 1 meli meli 335976 Aug 23 17:42 ibd
--rw-rw-r-- 1 meli meli  12402 Aug 23 17:42 imzml
+total 260
+-rw-rw-r-- 1 meli meli 248824 Sep 27 11:44 ibd
+-rw-rw-r-- 1 meli meli  12397 Sep 27 11:44 imzml
Binary file test-data/rdata_notfiltered.pdf has changed