# HG changeset patch # User galaxyp # Date 1585137939 14400 # Node ID d2ccd8348018ac4f74e25d6276fccecc5e02e1ee # Parent 528fb09022bec381d8b9a22ccf7560e0a159a7cd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" diff -r 528fb09022be -r d2ccd8348018 filtering.xml --- a/filtering.xml Fri Dec 13 13:55:48 2019 -0500 +++ b/filtering.xml Wed Mar 25 08:05:39 2020 -0400 @@ -1,12 +1,14 @@ - + tool for filtering mass spectrometry imaging data macros.xml - + + bioconductor-cardinal + r-base r-gridextra - r-ggplot2 - + r-ggplot2 + $outfile_imzml && ls -l "$outfile_imzml.files_path" >> $outfile_imzml ]]> @@ -37,29 +36,51 @@ library(ggplot2) library(gridExtra) -@READING_MSIDATA@ + + +## function to read RData files independent of filename +loadRData <- function(fileName){ +load(fileName) +get(ls()[ls() != "fileName"]) +} + +#if $infile.ext == 'imzml' + #if str($processed_cond.processed_file) == "processed": + msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE) + centroided(msidata) = $centroids + #else + msidata <- readImzML('infile', attach.only=TRUE) + centroided(msidata) = $centroids + #end if +#elif $infile.ext == 'analyze75' + msidata = readAnalyze('infile', attach.only=TRUE) + centroided(msidata) = $centroids +#else + msidata = loadRData('infile.RData') + msidata = as(msidata, "MSImagingExperiment") +#end if ########################### QC numbers ######################## ## Number of features (m/z) - maxfeatures = length(features(msidata)) + maxfeatures = nrow(msidata) ## Range m/z minmz = round(min(mz(msidata)), digits=2) maxmz = round(max(mz(msidata)), digits=2) ## Number of spectra (pixels) - pixelcount = length(pixels(msidata)) + pixelcount = ncol(msidata) ## Range x coordinates - minimumx = min(coord(msidata)[,1]) - maximumx = max(coord(msidata)[,1]) + minimumx = min(coord(msidata)\$x) + maximumx = max(coord(msidata)\$x) ## Range y coordinates - minimumy = min(coord(msidata)[,2]) - maximumy = max(coord(msidata)[,2]) + minimumy = min(coord(msidata)\$y) + maximumy = max(coord(msidata)\$y) ## Store features for QC plot featuresinfile = mz(msidata) - all_df = cbind(coord(msidata)[,1:2], rep("removed pixels", times=ncol(msidata))) - colnames(all_df)[3] = "annotation" + all_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, rep("removed pixels", times=ncol(msidata))) + colnames(all_df) = c("x", "y", "annotation") ## Next steps will only run if there are more than 0 pixels/features in the file @@ -92,7 +113,7 @@ error=function(cond) { ## in case all coordinates were outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data message("Error during pixel filtering") - message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool)") + message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool") stop(call.=FALSE) } ) @@ -142,9 +163,9 @@ ## dataframe for QC of pixel distribution - remaining_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata))) - colnames(remaining_df)[3] = "annotation" - position_df = rbind(all_df, remaining_df) + remaining_df = data.frame(as.numeric(coord(msidata)\$x), as.numeric(coord(msidata)\$y), rep("remaining pixels", times=ncol(msidata))) + colnames(remaining_df) = c("x", "y", "annotation") + position_df = rbind(all_df, remaining_df) position_df[row.names(unique(position_df[,c("x", "y")])),] position_df\$annotation = factor(position_df\$annotation) gc() @@ -205,7 +226,7 @@ ## in case all provided m/z values were outside the m/z range ## tool is stopped to avoid continuing with wrong data message("Error during m/z filtering") - message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)") + message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset (this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)") stop(call.=FALSE) } ) @@ -262,8 +283,11 @@ #end if current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus)) mass_to_remove = append(mass_to_remove, current_mass)} - msidata= msidata[-mass_to_remove, ] - validmz = numberfeatures - nrow(msidata) + mass_to_keep = setdiff(1:nrow(msidata),mass_to_remove) + + msidata= msidata[mass_to_keep, ] + validmz = maxfeatures - nrow(msidata) + ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data if (nrow(msidata) == 0) { @@ -278,7 +302,6 @@ - ######################## No m/z filtering ############################## #elif str($features_cond.features_filtering) == "none": @@ -304,18 +327,18 @@ #################### QC numbers ####################### ## Number of features (m/z) -maxfeatures2 = length(features(msidata)) +maxfeatures2 = nrow(msidata) ## Range m/z minmz2 = round(min(mz(msidata)), digits=2) maxmz2 = round(max(mz(msidata)), digits=2) ## Number of spectra (pixels) -pixelcount2 = length(pixels(msidata)) +pixelcount2 = ncol(msidata) ## Range x coordinates -minimumx2 = min(coord(msidata)[,1]) -maximumx2 = max(coord(msidata)[,1]) +minimumx2 = min(coord(msidata)\$x) +maximumx2 = max(coord(msidata)\$x) ## Range y coordinates -minimumy2 = min(coord(msidata)[,2]) -maximumy2 = max(coord(msidata)[,2]) +minimumy2 = min(coord(msidata)\$y) +maximumy2 = max(coord(msidata)\$y) properties = c("Number of m/z features", "Range of m/z values", @@ -347,7 +370,7 @@ pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12) plot(0,type='n',axes=FALSE,ann=FALSE) -title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name")) +title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.element_identifier")) grid.table(property_df, rows= NULL) ## QC report only when pixels/features are left @@ -362,35 +385,39 @@ ggtitle("Spatial orientation of filtered pixels")+ theme_bw()+ theme(plot.title = element_text(hjust = 0.5))+ - theme(legend.position="bottom",legend.direction="vertical") + theme(legend.position="bottom",legend.direction="vertical")+ + guides(fill=guide_legend(ncol=5,byrow=TRUE)) print(pixel_image) - ### plot features which are removed - hist(mz(msidata), xlab="m/z", main="Kept m/z values") - #if str($features_cond.features_filtering) == "none": - print("no difference histogram as no m/z filtering took place") - #else: - if (isTRUE(all.equal(featuresinfile, mz(msidata)))){ - print("No difference in m/z values before and after filtering, no histogram drawn") - }else{ - hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")} - #end if + + ### visual mz feature control + + kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata))) + colnames(kept_df) = c("mz", "legend") + + mz_removed = setdiff(featuresinfile, mz(msidata)) + removed_df = data.frame(mz_removed, rep("removed m/z", length(mz_removed))) + colnames(removed_df) = c("mz", "legend") + histogram_df = rbind(removed_df,kept_df) + + histogram_mz= ggplot(histogram_df, aes(x=mz, fill=legend)) + + geom_histogram()+ theme_bw()+ + theme(plot.title = element_text(hjust = 0.5))+ + theme(legend.position="bottom",legend.direction="vertical")+ + labs(title="Overview of filtered m/z", x="m/z", y = "count") + + guides(fill=guide_legend(ncol=5,byrow=TRUE)) + print(histogram_mz) + dev.off() ## save msidata as imzML file, will only work if there is at least 1 m/z left - #if str($imzml_output) == "imzml_format": if (maxfeatures2 > 0){ ## make sure that coordinates are integers coord(msidata)\$y = as.integer(coord(msidata)\$y) coord(msidata)\$x = as.integer(coord(msidata)\$x) writeImzML(msidata, "out")} - #elif str($imzml_output) == "rdata_format": - ## save msidata as Rfile - iData(msidata) = iData(msidata)[] - save(msidata, file="$outfile_rdata") - #end if }else{ @@ -448,20 +475,10 @@ - - - - - - imzml_output =='imzml_format' - - - imzml_output == 'rdata_format' - + @@ -475,10 +492,9 @@ - - + @@ -488,10 +504,9 @@ - - + @@ -506,34 +521,51 @@ - - + - - + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - 1.12.1 - - - - bioconductor-cardinal - r-base - - - - - - /dev/null | grep -v -i "WARNING: ") - ]]> - - - - - - - - - - - - 0, for if conditions - npeaks= sum(spectra(msidata)>0, na.rm=TRUE) - ## Number of NA in spectra matrix - NAcount = sum(is.na(spectra(msidata))) - ## Number of NA in spectra matrix - infcount = sum(is.infinite(spectra(msidata))) - ## Number of duplicated coordinates - dupl_coord = sum(duplicated(coord(msidata))) - - properties = c("Number of m/z features", - "Range of m/z values", - "Number of pixels", - "Range of x coordinates", - "Range of y coordinates", - "Range of intensities", - "Number of NA intensities", - "Number of Inf intensities", - "Number of duplicated coordinates") - - values = c(paste0(maxfeatures), - paste0(minmz, " - ", maxmz), - paste0(pixelcount), - paste0(minimumx, " - ", maximumx), - paste0(minimumy, " - ", maximumy), - paste0(minint, " - ", maxint), - paste0(NAcount), - paste0(infcount), - paste0(dupl_coord)) - - property_df = data.frame(properties, values) - ]]> - - `_ - ]]> - `_ - - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) - - Cardinal "MSImageSet" data saved as .RData - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1093/bioinformatics/btv146 - - - - - - - - - - - - - - - - + + 1.12.1 + + + + bioconductor-cardinal + r-base + + + + + + /dev/null | grep -v -i "WARNING: ") + ]]> + + + + + + + + + + + + 0, for if conditions + npeaks= sum(spectra(msidata)>0, na.rm=TRUE) + ## Number of NA in spectra matrix + NAcount = sum(is.na(spectra(msidata))) + ## Number of NA in spectra matrix + infcount = sum(is.infinite(spectra(msidata))) + ## Number of duplicated coordinates + dupl_coord = sum(duplicated(coord(msidata))) + + properties = c("Number of m/z features", + "Range of m/z values", + "Number of pixels", + "Range of x coordinates", + "Range of y coordinates", + "Range of intensities", + "Number of NA intensities", + "Number of Inf intensities", + "Number of duplicated coordinates") + + values = c(paste0(maxfeatures), + paste0(minmz, " - ", maxmz), + paste0(pixelcount), + paste0(minimumx, " - ", maximumx), + paste0(minimumy, " - ", maximumy), + paste0(minint, " - ", maxint), + paste0(NAcount), + paste0(infcount), + paste0(dupl_coord)) + + property_df = data.frame(properties, values) + ]]> + + `_ + ]]> + `_ + - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) + - Cardinal "MSImageSet" data saved as .RData + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btv146 + + + + + + + + + + + + + + + + + + + + + + diff -r 528fb09022be -r d2ccd8348018 test-data/Analyze75.hdr diff -r 528fb09022be -r d2ccd8348018 test-data/Analyze75.img diff -r 528fb09022be -r d2ccd8348018 test-data/Analyze75.t2m diff -r 528fb09022be -r d2ccd8348018 test-data/Example_Continuous.ibd diff -r 528fb09022be -r d2ccd8348018 test-data/Example_Continuous.imzML diff -r 528fb09022be -r d2ccd8348018 test-data/analyze75_filtered2.pdf Binary file test-data/analyze75_filtered2.pdf has changed diff -r 528fb09022be -r d2ccd8348018 test-data/imzml_filtered3.pdf Binary file test-data/imzml_filtered3.pdf has changed diff -r 528fb09022be -r d2ccd8348018 test-data/imzml_filtered4.pdf Binary file test-data/imzml_filtered4.pdf has changed diff -r 528fb09022be -r d2ccd8348018 test-data/imzml_filtered5.pdf Binary file test-data/imzml_filtered5.pdf has changed diff -r 528fb09022be -r d2ccd8348018 test-data/imzml_filtered8.pdf Binary file test-data/imzml_filtered8.pdf has changed diff -r 528fb09022be -r d2ccd8348018 test-data/out3.ibd Binary file test-data/out3.ibd has changed diff -r 528fb09022be -r d2ccd8348018 test-data/out3.imzml --- a/test-data/out3.imzml Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out3.imzml Wed Mar 25 08:05:39 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,18 +42,24 @@ - + - + + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + diff -r 528fb09022be -r d2ccd8348018 test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out3.imzml.txt Wed Mar 25 08:05:39 2020 -0400 @@ -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 diff -r 528fb09022be -r d2ccd8348018 test-data/out4.ibd Binary file test-data/out4.ibd has changed diff -r 528fb09022be -r d2ccd8348018 test-data/out4.imzml --- a/test-data/out4.imzml Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out4.imzml Wed Mar 25 08:05:39 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,18 +42,24 @@ - + - + + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + @@ -154,6 +165,8 @@ + + @@ -181,6 +194,8 @@ + + diff -r 528fb09022be -r d2ccd8348018 test-data/out4.imzml.txt --- a/test-data/out4.imzml.txt Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out4.imzml.txt Wed Mar 25 08:05:39 2020 -0400 @@ -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 diff -r 528fb09022be -r d2ccd8348018 test-data/out5.ibd Binary file test-data/out5.ibd has changed diff -r 528fb09022be -r d2ccd8348018 test-data/out5.imzml --- a/test-data/out5.imzml Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out5.imzml Wed Mar 25 08:05:39 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,18 +42,24 @@ - + - + + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + @@ -154,6 +165,8 @@ + + @@ -181,6 +194,8 @@ + + @@ -208,6 +223,8 @@ + + diff -r 528fb09022be -r d2ccd8348018 test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out5.imzml.txt Wed Mar 25 08:05:39 2020 -0400 @@ -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 diff -r 528fb09022be -r d2ccd8348018 test-data/out6.ibd Binary file test-data/out6.ibd has changed diff -r 528fb09022be -r d2ccd8348018 test-data/out6.imzml --- a/test-data/out6.imzml Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out6.imzml Wed Mar 25 08:05:39 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,7 +42,7 @@ - + @@ -51,10 +50,16 @@ + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + @@ -154,6 +165,8 @@ + + @@ -181,6 +194,8 @@ + + @@ -208,6 +223,8 @@ + + @@ -235,6 +252,8 @@ + + @@ -262,6 +281,8 @@ + + @@ -289,6 +310,8 @@ + + diff -r 528fb09022be -r d2ccd8348018 test-data/out6.imzml.txt --- a/test-data/out6.imzml.txt Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out6.imzml.txt Wed Mar 25 08:05:39 2020 -0400 @@ -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 diff -r 528fb09022be -r d2ccd8348018 test-data/out7.ibd Binary file test-data/out7.ibd has changed diff -r 528fb09022be -r d2ccd8348018 test-data/out7.imzml --- a/test-data/out7.imzml Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out7.imzml Wed Mar 25 08:05:39 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,7 +42,7 @@ - + @@ -51,10 +50,16 @@ + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + @@ -154,6 +165,8 @@ + + @@ -181,6 +194,8 @@ + + @@ -208,6 +223,8 @@ + + @@ -235,6 +252,8 @@ + + @@ -262,6 +281,8 @@ + + @@ -289,6 +310,8 @@ + + diff -r 528fb09022be -r d2ccd8348018 test-data/out7.imzml.txt --- a/test-data/out7.imzml.txt Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/out7.imzml.txt Wed Mar 25 08:05:39 2020 -0400 @@ -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 diff -r 528fb09022be -r d2ccd8348018 test-data/out8.ibd Binary file test-data/out8.ibd has changed diff -r 528fb09022be -r d2ccd8348018 test-data/out8.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml Wed Mar 25 08:05:39 2020 -0400 @@ -0,0 +1,224 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 528fb09022be -r d2ccd8348018 test-data/out8.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml.txt Wed Mar 25 08:05:39 2020 -0400 @@ -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 diff -r 528fb09022be -r d2ccd8348018 test-data/preprocessing_results1.ibd Binary file test-data/preprocessing_results1.ibd has changed diff -r 528fb09022be -r d2ccd8348018 test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/preprocessing_results1.imzml Wed Mar 25 08:05:39 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,7 +42,7 @@ - + @@ -51,10 +50,16 @@ + + + + - + + + @@ -73,21 +78,23 @@ + + - - + + - - - + + + @@ -100,21 +107,23 @@ + + - - + + - - - + + + @@ -127,21 +136,23 @@ + + - - + + - - - + + + @@ -154,21 +165,23 @@ + + - - + + - - - + + + @@ -181,21 +194,23 @@ + + - - + + - - - + + + @@ -208,21 +223,23 @@ + + - - + + - - - + + + @@ -235,21 +252,23 @@ + + - - + + - - - + + + @@ -262,21 +281,23 @@ + + - - + + - - - + + + @@ -289,21 +310,23 @@ + + - - + + - - - + + + diff -r 528fb09022be -r d2ccd8348018 test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/preprocessing_results1.imzml.txt Wed Mar 25 08:05:39 2020 -0400 @@ -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 diff -r 528fb09022be -r d2ccd8348018 test-data/preprocessing_results1.pdf Binary file test-data/preprocessing_results1.pdf has changed diff -r 528fb09022be -r d2ccd8348018 test-data/preprocessing_results2.ibd Binary file test-data/preprocessing_results2.ibd has changed diff -r 528fb09022be -r d2ccd8348018 test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Fri Dec 13 13:55:48 2019 -0500 +++ b/test-data/preprocessing_results2.imzml Wed Mar 25 08:05:39 2020 -0400 @@ -9,8 +9,8 @@ - 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