# HG changeset patch # User galaxyp # Date 1585138397 14400 # Node ID 5bf056c0354e547c043fdcd94287d14158686ca5 # Parent ed9ed1e6cca2fd5db5e9e7719d550d1a34bbce01 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" diff -r ed9ed1e6cca2 -r 5bf056c0354e macros.xml --- a/macros.xml Fri Dec 13 13:57:13 2019 -0500 +++ b/macros.xml Wed Mar 25 08:13:17 2020 -0400 @@ -1,316 +1,322 @@ - - 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 ed9ed1e6cca2 -r 5bf056c0354e preprocessing.xml --- a/preprocessing.xml Fri Dec 13 13:57:13 2019 -0500 +++ b/preprocessing.xml Wed Mar 25 08:13:17 2020 -0400 @@ -1,15 +1,17 @@ - + mass spectrometry imaging preprocessing macros.xml - + + bioconductor-cardinal + r-base r-gridextra - r-ggplot2 - r-lattice - + r-ggplot2 + r-lattice + $outfile_imzml && ls -l "$outfile_imzml.files_path" >> $outfile_imzml @@ -37,12 +37,37 @@ library(lattice) library(ggplot2) -@READING_MSIDATA@ + + ## function to read RData files independent of filename + loadRData <- function(fileName){ + load(fileName) + get(ls()[ls() != "fileName"]) + } -@READING_MSIDATA_INRAM@ ###change out + #if $infile.ext == 'imzml' + #if str($processed_cond.processed_file) == "processed": + msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units") + centroided(msidata) = $centroids + #else + msidata <- readImzML('infile') + centroided(msidata) = $centroids + #end if + #elif $infile.ext == 'analyze75' + msidata = readAnalyze('infile') + centroided(msidata) = $centroids + #else + msidata = loadRData('infile.RData') + msidata = as(msidata, "MSImagingExperiment") + #end if + ## remove duplicated coordinates, otherwise peak picking and log2 transformation will fail -msidata <- msidata[,!duplicated(coord(msidata)[,1:2])] +msidata <- msidata[,!duplicated(coord(msidata)[,1:2])] + +## set variable to False +#set $used_peak_picking = False +#set $used_peak_alignment = False +#set $continuous_format = False if (ncol(msidata)>0 & nrow(msidata) >0){ @@ -63,12 +88,10 @@ vectorofactions = "inputdata" ## Choose random spectra for QC plots random_spectra = sample(pixels(msidata), 4, replace=FALSE) - par(mfrow = c(2, 2), oma=c(0,0,2,0)) - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + par(oma=c(0,0,2,0)) + print(plot(msidata, pixel=random_spectra)) title("Input spectra", outer=TRUE, line=0) - ############################### Preprocessing steps ########################### ############################################################################### @@ -80,7 +103,13 @@ print('Normalization') ##normalization + if (class(msidata) == "MSProcessedImagingExperiment"){ + msidata = as(msidata, "MSContinuousImagingExperiment") + } + msidata = normalize(msidata, method="tic") + msidata <- process(msidata, BPPARAM=MulticoreParam()) + ############################### QC ########################### @@ -91,9 +120,7 @@ normalized = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, normalized) vectorofactions = append(vectorofactions, "normalized") - par(mfrow = c(2, 2), oma=c(0,0,2,0)) - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + print(plot(msidata, pixel=random_spectra)) title("Spectra after normalization", outer=TRUE, line=0) ############################### Baseline reduction ########################### @@ -102,7 +129,12 @@ print('Baseline_reduction') ##baseline reduction + if (class(msidata) == "MSProcessedImagingExperiment"){ + msidata = as(msidata, "MSContinuousImagingExperiment") + } + msidata = reduceBaseline(msidata, method="median", blocks=$method.methods_conditional.blocks_baseline, spar=$method.methods_conditional.spar_baseline) + msidata <- process(msidata, BPPARAM=MulticoreParam()) ############################### QC ########################### @@ -113,8 +145,7 @@ baseline = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, baseline) vectorofactions = append(vectorofactions, "baseline red.") - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + print(plot(msidata, pixel=random_spectra)) title("Spectra after baseline reduction", outer=TRUE, line=0) ############################### Smoothing ########################### @@ -123,6 +154,11 @@ print('Smoothing') ## Smoothing + if (class(msidata) == "MSProcessedImagingExperiment"){ + msidata = as(msidata, "MSContinuousImagingExperiment") + } + + #if str( $method.methods_conditional.methods_for_smoothing.smoothing_method) == 'gaussian': print('gaussian smoothing') @@ -144,6 +180,7 @@ msidata = smoothSignal(msidata, method="$method.methods_conditional.methods_for_smoothing.smoothing_method", window=$method.methods_conditional.window_smoothing, coef = $method.methods_conditional.methods_for_smoothing.coefficients_ma_filter) #end if + msidata <- process(msidata, BPPARAM=MulticoreParam()) ############################### QC ########################### @@ -154,13 +191,13 @@ smoothed = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, smoothed) vectorofactions = append(vectorofactions, "smoothed") - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + print(plot(msidata, pixel=random_spectra)) title("Spectra after smoothing", outer=TRUE, line=0) ############################### Peak picking ########################### #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_picking': + #set $used_peak_picking = True print('Peak_picking') ## Peakpicking @@ -169,10 +206,10 @@ msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, spar=$method.methods_conditional.methods_for_picking.spar_picking) - #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'limpic': - print('limpic peakpicking') + #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'mad': + print('mad peakpicking') - msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method, thresh=$method.methods_conditional.methods_for_picking.tresh_picking) + msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method) #elif str( $method.methods_conditional.methods_for_picking.picking_method) == 'simple': print('simple peakpicking') @@ -180,6 +217,12 @@ msidata = peakPick(msidata, window = $method.methods_conditional.window_picking, blocks = $method.methods_conditional.blocks_picking, method='$method.methods_conditional.methods_for_picking.picking_method', SNR=$method.methods_conditional.SNR_picking_method) #end if + msidata <- process(msidata, BPPARAM=MulticoreParam()) + + #if str($method.methods_conditional.imzml_output) == "cont_format": + #set $continuous_format = True + #end if + ############################### QC ########################### @@ -190,45 +233,40 @@ picked = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, picked) vectorofactions = append(vectorofactions, "picked") - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + print(plot(msidata, pixel=random_spectra)) title("Spectra after peak picking", outer=TRUE, line=0) ############################### Peak alignment ########################### #elif str( $method.methods_conditional.preprocessing_method ) == 'Peak_alignment': + #set $used_peak_alignment = True print('Peak_alignment') ## Peakalignment - #if str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_noref': - - align_peak_reference = msidata - - #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table': + #if str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_table': align_reference_table = read.delim("$method.methods_conditional.align_ref_type.mz_tabular", header = $method.methods_conditional.align_ref_type.feature_header, stringsAsFactors = FALSE) + align_reference_column = align_reference_table[,$method.methods_conditional.align_ref_type.feature_column] - align_peak_reference = align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))] + + align_peak_reference = as.numeric(align_reference_column[align_reference_column>=min(mz(msidata)) & align_reference_column<=max(mz(msidata))]) if (length(align_peak_reference) == 0) {align_peak_reference = 0} - - #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_msidata_ref': + + msidata = peakAlign(msidata,tolerance =$method.methods_conditional.value_diffalignment, units = "$method.methods_conditional.units_diffalignment", ref=align_peak_reference) + - align_peak_reference = loadRData('$method.methods_conditional.align_ref_type.align_peaks_msidata') + #elif str( $method.methods_conditional.align_ref_type.align_reference_datatype) == 'align_noref': + + msidata = peakAlign(msidata,tolerance =$method.methods_conditional.value_diffalignment, units = "$method.methods_conditional.units_diffalignment") #end if - #if str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'diff': - print('diff peakalignment') - - msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',diff.max =$method.methods_conditional.methods_for_alignment.value_diffalignment, units = "$method.methods_conditional.methods_for_alignment.units_diffalignment", ref=align_peak_reference) + msidata <- process(msidata, BPPARAM=MulticoreParam()) - #elif str( $method.methods_conditional.methods_for_alignment.alignment_method) == 'DP': - print('DPpeakalignment') - - msidata = peakAlign(msidata, method='$method.methods_conditional.methods_for_alignment.alignment_method',gap = $method.methods_conditional.methods_for_alignment.gap_DPalignment, ref=align_peak_reference) - - #end if + #if str($method.methods_conditional.imzml_output) == "cont_format": + #set $continuous_format = True + #end if ############################### QC ########################### @@ -239,8 +277,7 @@ aligned = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, aligned) vectorofactions = append(vectorofactions, "aligned") - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + print(plot(msidata, pixel=random_spectra)) title("Spectra after alignment", outer=TRUE, line=0) ############################### Peak filtering ########################### @@ -248,7 +285,8 @@ #elif str( $method.methods_conditional.preprocessing_method) == 'Peak_filtering': print('Peak_filtering') - msidata = peakFilter(msidata, method='freq', freq.min = $method.methods_conditional.frequ_filtering) + msidata = peakFilter(msidata, freq.min = $method.methods_conditional.frequ_filtering) + msidata <- process(msidata, BPPARAM=MulticoreParam()) ############################### QC ########################### @@ -259,8 +297,7 @@ filtered = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, filtered) vectorofactions = append(vectorofactions, "filtered") - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + print(plot(msidata, pixel=random_spectra)) title("Spectra after filtering", outer=TRUE, line=0) ############################### Data reduction ########################### @@ -268,6 +305,9 @@ #elif str( $method.methods_conditional.preprocessing_method) == 'Data_reduction': print('Data_reduction') + ## these functions only work on MSImageSet + msidata = as(msidata, "MSImageSet") + #if str( $method.methods_conditional.methods_for_reduction.reduction_method) == 'bin': print('bin reduction') @@ -302,6 +342,10 @@ msidata = reduceDimension(msidata, method="peaks", ref=peak_reference, type="$method.methods_conditional.methods_for_reduction.peaks_type") #end if + + ## coercition into new format + msidata = as(msidata, "MSImagingExperiment") + ############################### QC ########################### maxfeatures =nrow(msidata) @@ -311,8 +355,7 @@ reduced = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, reduced) vectorofactions = append(vectorofactions, "reduced") - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + print(plot(msidata, pixel=random_spectra)) title("Spectra after data reduction", outer=TRUE, line=0) ############################### Transformation ########################### @@ -320,14 +363,15 @@ #elif str( $method.methods_conditional.preprocessing_method) == 'Transformation': print('Transformation') - ## convert data into R matrix what brings it automatically into memory and can take some take but next steps need R matrix - ##iData(msidata) <- iData(msidata)[] + if (class(msidata) == "MSProcessedImagingExperiment"){ + msidata = as(msidata, "MSContinuousImagingExperiment") + } #if str( $method.methods_conditional.transf_conditional.trans_type) == 'log2': print('log2 transformation') ## replace 0 with NA to prevent Inf - spectra_df = spectra(msidata)[] ## convert into R matrix + spectra_df = spectra(msidata) ## convert into R matrix spectra_df[spectra_df ==0] = NA print(paste0("Number of 0 which were converted into NA:",sum(is.na(spectra_df)))) spectra(msidata) = spectra_df @@ -341,7 +385,7 @@ #elif str( $method.methods_conditional.transf_conditional.trans_type) == 'sqrt': print('squareroot transformation') - spectra(msidata) = sqrt(spectra(msidata)[]) + spectra(msidata) = sqrt(spectra(msidata)) #end if @@ -354,8 +398,7 @@ transformed = c(minmz, maxmz,maxfeatures, pixelcount) QC_numbers= cbind(QC_numbers, transformed) vectorofactions = append(vectorofactions, "transformed") - for (random_sample in 1:length(random_spectra)){ - plot(msidata, pixel=random_spectra[random_sample], main=paste0("spectrum ", names(random_spectra)[random_sample]))} + print(plot(msidata, pixel=random_spectra)) title("Spectra after transformation", outer=TRUE, line=0) #end if @@ -366,22 +409,25 @@ ## save msidata as imzML file, will only work if there is at least 1 m/z left - #if str($imzml_output) == "imzml_format": if (nrow(msidata) > 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($imzml_output) == "rdata_format": - ## save as (.RData) - iData(msidata) = iData(msidata)[] - save(msidata, file="$outfile_rdata") - #end if + #if $used_peak_picking: + #if $continuous_format: + msidata = as(msidata, "MSContinuousImagingExperiment") + #end if + #elif $used_peak_alignment + #if $continuous_format: + msidata = as(msidata, "MSContinuousImagingExperiment") + #end if + #end if + writeImzML(msidata, "out") + } plot(0,type='n',axes=FALSE,ann=FALSE) rownames(QC_numbers) = c("min m/z", "max mz", "# features", "# spectra") grid.table(t(QC_numbers)) - dev.off() }else{ @@ -395,7 +441,7 @@ - + @@ -404,7 +450,16 @@ - + + + + + + + + + + @@ -438,16 +493,16 @@ label="Window size"/> - - + - + @@ -457,50 +512,32 @@ applied to the spectrum in order to decide the cutoffs for throwing away false noise spikes that might occur inside peaks"/> - - - + + - - - - - - - - - - - - - - - - + + + + + - - - - + - + @@ -563,19 +600,9 @@ - - - - - - imzml_output=='imzml_format' - - - imzml_output == 'rdata_format' - + @@ -585,7 +612,7 @@ - + @@ -613,15 +640,12 @@ - - - - + @@ -632,10 +656,9 @@ - - + @@ -655,15 +678,11 @@ - - - - - + @@ -673,7 +692,7 @@ - + @@ -683,21 +702,29 @@ - + + + + - - - + + + + + + + + + - - + @@ -706,35 +733,49 @@ + - + + + + - - + - + + + + + + - - - - + + + - - + + + + + + + + + @@ -752,7 +793,7 @@ **Options** -- Normalization: Normalization of intensities to total ion current (TIC) +- Normalization: Normalization of intensities to total ion current (TIC) or to root-mean-square (RMS) - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets) - Smoothing: Smoothing of the peaks reduces noise and improves peak detection - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards) @@ -761,14 +802,9 @@ - Data reduction: binning, resampling or peak filtering to reduce data - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. -**Tips** - -- Peak alignment works only after peak picking -- Peak filtering works only on centroided data (peak picking and alignment or Data reduction peaks - **Output** -- MSI data as imzML file or .RData (can be read with the Cardinal package in R) +- MSI data as continuous imzML file (option to output processed imzML file only after peak picking/peak alignment; but is not yet compatible with other MSI tools) - pdf with key values and four random mass spectra after each processing step ]]> diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/Analyze75.hdr diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/Analyze75.img diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/Analyze75.t2m diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/Example_Continuous.ibd diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/Example_Continuous.imzML diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/analyze75_filtered2.pdf Binary file test-data/analyze75_filtered2.pdf has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/imzml_filtered3.pdf Binary file test-data/imzml_filtered3.pdf has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/imzml_filtered4.pdf Binary file test-data/imzml_filtered4.pdf has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/imzml_filtered5.pdf Binary file test-data/imzml_filtered5.pdf has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/imzml_filtered8.pdf Binary file test-data/imzml_filtered8.pdf has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/out3.ibd Binary file test-data/out3.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/out3.imzml --- a/test-data/out3.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out3.imzml Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out3.imzml.txt Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out4.ibd Binary file test-data/out4.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/out4.imzml --- a/test-data/out4.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out4.imzml Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out4.imzml.txt --- a/test-data/out4.imzml.txt Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out4.imzml.txt Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out5.ibd Binary file test-data/out5.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/out5.imzml --- a/test-data/out5.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out5.imzml Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out5.imzml.txt Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out6.ibd Binary file test-data/out6.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/out6.imzml --- a/test-data/out6.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out6.imzml Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out6.imzml.txt --- a/test-data/out6.imzml.txt Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out6.imzml.txt Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out7.ibd Binary file test-data/out7.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/out7.imzml --- a/test-data/out7.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out7.imzml Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out7.imzml.txt --- a/test-data/out7.imzml.txt Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/out7.imzml.txt Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/out8.ibd Binary file test-data/out8.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/out8.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml Wed Mar 25 08:13:17 2020 -0400 @@ -0,0 +1,224 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/out8.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml.txt Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results1.ibd Binary file test-data/preprocessing_results1.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/preprocessing_results1.imzml Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/preprocessing_results1.imzml.txt Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results1.pdf Binary file test-data/preprocessing_results1.pdf has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results2.ibd Binary file test-data/preprocessing_results2.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/preprocessing_results2.imzml Wed Mar 25 08:13:17 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,18 +42,24 @@ - + - + + + + + - + + + @@ -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 @@ + + - - + + - - - + + + @@ -316,21 +339,23 @@ + + - - + + - - - + + + @@ -343,21 +368,23 @@ + + - - + + - - - + + + @@ -370,21 +397,23 @@ + + - - + + - - - + + + diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/preprocessing_results2.imzml.txt Wed Mar 25 08:13:17 2020 -0400 @@ -1,4 +1,4 @@ imzML file: -total 80 --rw-r--r-- 1 meli meli 54720 Feb 24 14:12 ibd --rw-r--r-- 1 meli meli 21132 Feb 24 14:12 imzml +total 64 +-rw-r--r-- 1 meli meli 37404 Mär 24 10:40 ibd +-rw-r--r-- 1 meli meli 22796 Mär 24 10:40 imzml diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results2.pdf Binary file test-data/preprocessing_results2.pdf has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results3.ibd Binary file test-data/preprocessing_results3.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/preprocessing_results3.imzml Wed Mar 25 08:13:17 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 ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/preprocessing_results3.imzml.txt Wed Mar 25 08:13:17 2020 -0400 @@ -1,4 +1,4 @@ imzML file: -total 36 --rw-r--r-- 1 meli meli 14216 Feb 24 14:12 ibd --rw-r--r-- 1 meli meli 16824 Feb 24 14:12 imzml +total 24 +-rw-r--r-- 1 meli meli 136 Mär 24 11:10 ibd +-rw-r--r-- 1 meli meli 18088 Mär 24 11:10 imzml diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results3.pdf Binary file test-data/preprocessing_results3.pdf has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results4.ibd Binary file test-data/preprocessing_results4.ibd has changed diff -r ed9ed1e6cca2 -r 5bf056c0354e test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Fri Dec 13 13:57:13 2019 -0500 +++ b/test-data/preprocessing_results4.imzml Wed Mar 25 08:13:17 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 @@