| Previous changeset 16:bb6397b94018 (2023-04-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c |
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modified:
data_exporter.xml macros.xml test-data/ComBat_results_Example_processed_file.ibd test-data/ComBat_results_Example_processed_file.imzml test-data/Combat_40pixel.ibd test-data/Combat_40pixel.imzML test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_imzml_shortreport.pdf test-data/annotation_40pixel.tabular test-data/centroids_rdata.pdf test-data/classes_proc.tabular test-data/classes_ssc.tabular test-data/cluster_skm.RData test-data/cluster_skm.tabular test-data/dgmm_test1.pdf test-data/dgmm_test2.RData test-data/dgmm_test2.pdf test-data/estimates_r1_k6_mz1135.93347167969.tabular test-data/estimates_r2_k10_mz1200.46533203125.tabular test-data/features_test6.tabular test-data/imzml_filtered8.pdf test-data/inputcalibrantfile1.tabular test-data/inputcalibrantfile2.txt test-data/kmeans_analyze.pdf test-data/out8.ibd test-data/out8.imzml test-data/pixel_out4.tabular test-data/pixels_test2.tabular test-data/pixels_test4.tabular test-data/pixels_test6.tabular test-data/pixels_test7.tabular test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.pdf test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.pdf test-data/preprocessing_results5.ibd test-data/preprocessing_results5.imzml test-data/preprocessing_results5.pdf test-data/preprocessing_results_combat_40pixel.ibd test-data/preprocessing_results_combat_40pixel.imzml test-data/preprocessing_results_combat_40pixel.pdf test-data/probability_r1_k6_mz1023.70806884766.tabular test-data/probability_r2_k10_mz1135.93347167969.tabular test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata test-data/toplabels_skm.tabular test-data/toplabels_ssc.tabular |
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added:
test-data/ComBat_results_Example_processed_file.html test-data/ComBat_results_Example_processed_file.pdf test-data/best_r_test5.txt test-data/best_s_test5.txt test-data/cluster_skm.rdata test-data/coefficients_test2.tabular test-data/coefficients_test4.tabular test-data/coefficients_test7.tabular test-data/loadings_and_weights_test2.tabular test-data/loadings_and_weights_test4.tabular test-data/loadings_and_weights_test7.tabular test-data/out8.html test-data/preprocessing_results1.html test-data/preprocessing_results2.html test-data/preprocessing_results4.html test-data/preprocessing_results5.html test-data/preprocessing_results_combat_40pixel.html |
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removed:
test-data/ComBat_results_Example_processed_file_preprocessing.pdf test-data/QC_rdata.pdf test-data/centroids_proc.pdf test-data/features_out4.tabular test-data/features_test1.tabular test-data/features_test2.tabular test-data/features_test3.tabular test-data/features_test4.tabular test-data/features_test5.tabular test-data/features_test7.tabular test-data/pixels_test1.tabular test-data/pixels_test3.tabular test-data/pixels_test5.tabular test-data/toplabels_proc.tabular |
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| diff -r bb6397b94018 -r 56da27be956a data_exporter.xml --- a/data_exporter.xml Wed Apr 19 22:52:19 2023 +0000 +++ b/data_exporter.xml Thu Jul 04 13:34:08 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="cardinal_data_exporter" name="MSI data exporter" version="@VERSION@.0"> +<tool id="cardinal_data_exporter" name="MSI data exporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> <description> exports imzML and Analyze7.5 to tabular files </description> @@ -102,7 +102,7 @@ count = 1 for (subsample in levels(msidata\$annotation)){ subsample_pixels = msidata[,msidata\$annotation == subsample] - subsample_calc = rowMeans(spectra(subsample_pixels), na.rm=TRUE) + subsample_calc = rowMeans(as.matrix(spectra(subsample_pixels)), na.rm=TRUE) sample_matrix = cbind(sample_matrix, subsample_calc) count = count+1} sample_matrix_mean = cbind(mz_names,sample_matrix) @@ -117,7 +117,7 @@ count = 1 for (subsample in levels(msidata\$annotation)){ subsample_pixels = msidata[,msidata\$annotation == subsample] - subsample_calc = apply(spectra(subsample_pixels),1,median, na.rm=TRUE) + subsample_calc = apply(as.matrix(spectra(subsample_pixels)),1,median, na.rm=TRUE) sample_matrix = cbind(sample_matrix, subsample_calc) count = count+1} sample_matrix_median = cbind(mz_names,sample_matrix) @@ -190,13 +190,13 @@ for (mass in 1:length(inputcalibrantmasses)){ filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],] - if (nrow(filtered_data) > 1 & sum(spectra(filtered_data),na.rm=TRUE) > 0){ + if (nrow(filtered_data) > 1 & sum(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0){ ## intensity of all m/z > 0 - intensity_sum = colSums(spectra(filtered_data), na.rm=TRUE) > 0 + intensity_sum = colSums(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0 - }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data), na.rm=TRUE) > 0){ + }else if(nrow(filtered_data) == 1 & sum(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0){ ## intensity of only m/z > 0 - intensity_sum = spectra(filtered_data) > 0 + intensity_sum = as.matrix(spectra(filtered_data)) > 0 }else{ intensity_sum = rep(FALSE, ncol(filtered_data))} ## for each pixel add sum of intensities > 0 in the given m/z range @@ -343,7 +343,11 @@ <param name="feature_header" value="False"/> <param name="plusminus_ppm" value="200"/> </conditional> - <output name="feature_output" file="features_out4.tabular"/> + <output name="feature_output"> + <assert_contents> + <has_text text="100.120072029209"/> + </assert_contents> + </output> <output name="pixel_output" file="pixel_out4.tabular"/> </test> </tests> |
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| diff -r bb6397b94018 -r 56da27be956a macros.xml --- a/macros.xml Wed Apr 19 22:52:19 2023 +0000 +++ b/macros.xml Thu Jul 04 13:34:08 2024 +0000 |
| [ |
| @@ -1,10 +1,20 @@ <macros> - <token name="@VERSION@">2.10.0</token> + <token name="@TOOL_VERSION@">3.4.3</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> - <!--requirement type="package" version="3.6.1">r-base</requirement--> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-cardinal</requirement> + <requirement type="package" version="2.3">r-gridextra</requirement> + <requirement type="package" version="3.5.1">r-ggplot2</requirement> + <requirement type="package" version="0.14.1">r-maldiquantforeign</requirement> + <requirement type="package" version="1.22.2">r-maldiquant</requirement> + <requirement type="package" version="3.50.0">bioconductor-sva</requirement> + <requirement type="package" version="1.1.0.1">r-randomcolor</requirement> + <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement> + <requirement type="package" version="2.23_24">r-kernsmooth</requirement> + <requirement type="package" version="1.3.0">r-scales</requirement> + <requirement type="package" version="1.0.12">r-pheatmap</requirement> <yield/> </requirements> </xml> @@ -17,12 +27,12 @@ <token name="@INPUT_LINKING@"><![CDATA[ #if $infile.ext == 'imzml' - ln -s '${infile.extra_files_path}/imzml' infile.imzML && - ln -s '${infile.extra_files_path}/ibd' infile.ibd && + cp '${infile.extra_files_path}/imzml' infile.imzML && + cp '${infile.extra_files_path}/ibd' infile.ibd && #elif $infile.ext == 'analyze75' - ln -s '${infile.extra_files_path}/hdr' infile.hdr && - ln -s '${infile.extra_files_path}/img' infile.img && - ln -s '${infile.extra_files_path}/t2m' infile.t2m && + cp '${infile.extra_files_path}/hdr' infile.hdr && + cp '${infile.extra_files_path}/img' infile.img && + cp '${infile.extra_files_path}/t2m' infile.t2m && #else ln -s $infile infile.RData && #end if @@ -38,13 +48,13 @@ get(ls()[ls() != "fileName"]) } + #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": msidata <- readImzML('infile', resolution=$processed_cond.accuracy, attach.only=TRUE, units = "$processed_cond.units") - msidata = collect(msidata, as.matrix=TRUE) ##coercion to continuous centroided(msidata) = $centroids #else - msidata <- readImzML('infile', attach.only=TRUE) + msidata <- readImzML('infile') centroided(msidata) = $centroids #end if #elif $infile.ext == 'analyze75' @@ -95,7 +105,7 @@ msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE) centroided(msidata) = $centroids #else - msidata <- readImzML('infile', attach.only=TRUE) + msidata <- readImzML('infile') centroided(msidata) = $centroids #end if #elif $infile.ext == 'analyze75' @@ -117,13 +127,13 @@ <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 |
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| diff -r bb6397b94018 -r 56da27be956a test-data/ComBat_results_Example_processed_file.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ComBat_results_Example_processed_file.html Thu Jul 04 13:34:08 2024 +0000 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 428 +-rw-r--r-- 1 maren maren 415936 Jun 20 14:23 ibd +-rw-r--r-- 1 maren maren 18243 Jun 20 14:23 imzml |
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| diff -r bb6397b94018 -r 56da27be956a test-data/ComBat_results_Example_processed_file.ibd |
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| diff -r bb6397b94018 -r 56da27be956a test-data/ComBat_results_Example_processed_file.imzml --- a/test-data/ComBat_results_Example_processed_file.imzml Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/ComBat_results_Example_processed_file.imzml Thu Jul 04 13:34:08 2024 +0000 |
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| b'@@ -9,8 +9,8 @@\n \t\t<fileContent>\n \t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="82e7db90-df72-41f8-9ca7-7a19e966d5c1" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="259aa4b90129abb2f1f3107cf123f28d7c744f0c" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="bff0e5f4-5dea-4fc8-90c4-dd30b8464a7a" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="964c9332a0878edc5a2fc6420627334a9a43d442" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -42,16 +42,12 @@\n \t\t</sample>\n \t</sampleList>\n \t<softwareList count="1">\n-\t\t<software id="Cardinal" 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| @@ -1,10 +1,10 @@ -pixel names x y r = 1, k = 2 r = 1, k = 3 r = 2, k = 2 r = 2, k = 3 r = 3, k = 2 r = 3, k = 3 +pixel names x y r=1, k=2 r=1, k=3 r=2, k=2 r=2, k=3 r=3, k=2 r=3, k=3 xy_1_1 1 1 2 2 2 2 2 2 -xy_2_1 2 1 1 1 1 1 1 1 -xy_3_1 3 1 1 1 1 1 1 1 +xy_2_1 2 1 2 3 2 2 2 2 +xy_3_1 3 1 1 3 1 1 1 1 xy_1_2 1 2 2 2 2 2 2 2 -xy_2_2 2 2 1 1 1 1 1 1 -xy_3_2 3 2 1 1 1 1 1 1 -xy_1_3 1 3 1 1 1 1 1 1 -xy_2_3 2 3 1 1 1 1 1 1 -xy_3_3 3 3 1 3 1 3 1 3 +xy_2_2 2 2 1 3 1 3 1 3 +xy_3_2 3 2 1 3 1 1 1 1 +xy_1_3 1 3 1 1 1 3 1 3 +xy_2_3 2 3 1 1 1 3 1 3 +xy_3_3 3 3 1 1 1 1 1 1 |
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|
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/coefficients_test7.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coefficients_test7.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
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| diff -r bb6397b94018 -r 56da27be956a test-data/estimates_r1_k6_mz1135.93347167969.tabular --- a/test-data/estimates_r1_k6_mz1135.93347167969.tabular Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/estimates_r1_k6_mz1135.93347167969.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
| @@ -1,4 +1,4 @@ group class mean var -files_ 1 0.172268980321456 0.133976695047921 -files_ 2 4.88607208725277 0.301220362077463 -files_ 3 6.64940193494161 0.752878508867188 +files_ 1 0.224949111319976 0.133976695047921 +files_ 2 4.8214570634499 0.301220362077463 +files_ 3 6.6086885724357 0.752878508867188 |
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| diff -r bb6397b94018 -r 56da27be956a test-data/estimates_r2_k10_mz1200.46533203125.tabular --- a/test-data/estimates_r2_k10_mz1200.46533203125.tabular Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/estimates_r2_k10_mz1200.46533203125.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
| @@ -1,6 +1,6 @@ group class mean var -bg 1 0.216553505243044 0.158967083338173 -bg 2 4.13395686852547 0.859771560896229 -circle 3 3.16694802842791 0.372813860593546 -circle 4 4.48944198265987 1.71739690046886 +bg 1 0.24404370080711 0.158967083338173 +bg 2 3.70987357402502 0.859771560896229 +circle 3 3.20052414013949 0.373783892349068 +circle 4 5.55910670518051 1.71747870891981 square 5 3.8928901507304 1.21620428871296 |
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| diff -r bb6397b94018 -r 56da27be956a test-data/features_out4.tabular --- a/test-data/features_out4.tabular Wed Apr 19 22:52:19 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,10399 +0,0 @@\n-mz_names\tmz\tsample_mean\tsample_median\tsample_sd\tsample_sem\tintensity_sum\tnumber_peaks\n-mz_100\t100\t0\t0\t0\tNA\t0\t0\n-mz_100.0200020002\t100.0200020002\t0\t0\t0\tNA\t0\t0\n-mz_100.0400080012\t100.0400080012\t0\t0\t0\tNA\t0\t0\n-mz_100.060018003801\t100.060018003801\t0\t0\t0\tNA\t0\t0\n-mz_100.080032008802\t100.080032008802\t0\t0\t0\tNA\t0\t0\n-mz_100.100050017005\t100.100050017005\t0\t0\t0\tNA\t0\t0\n-mz_100.120072029209\t100.120072029209\t0\t0\t0\tNA\t0\t0\n-mz_100.140098046217\t100.140098046217\t0\t0\t0\tNA\t0\t0\n-mz_100.160128068828\t100.160128068828\t0\t0\t0\tNA\t0\t0\n-mz_100.180162097845\t100.180162097845\t0\t0\t0\tNA\t0\t0\n-mz_100.200200134068\t100.200200134068\t0\t0\t0\tNA\t0\t0\n-mz_100.220242178299\t100.220242178299\t0\t0\t0\tNA\t0\t0\n-mz_100.24028823134\t100.24028823134\t0\t0\t0\tNA\t0\t0\n-mz_100.260338293993\t100.260338293993\t0\t0\t0\tNA\t0\t0\n-mz_100.280392367059\t100.280392367059\t0\t0\t0\tNA\t0\t0\n-mz_100.300450451341\t100.300450451341\t0\t0\t0\tNA\t0\t0\n-mz_100.320512547641\t100.320512547641\t0\t0\t0\tNA\t0\t0\n-mz_100.340578656761\t100.340578656761\t0\t0\t0\tNA\t0\t0\n-mz_100.360648779505\t100.360648779505\t0\t0\t0\tNA\t0\t0\n-mz_100.380722916674\t100.380722916674\t0\t0\t0\tNA\t0\t0\n-mz_100.400801069073\t100.400801069073\t0\t0\t0\tNA\t0\t0\n-mz_100.420883237504\t100.420883237504\t0\t0\t0\tNA\t0\t0\n-mz_100.44096942277\t100.44096942277\t0\t0\t0\tNA\t0\t0\n-mz_100.461059625675\t100.461059625675\t0\t0\t0\tNA\t0\t0\n-mz_100.481153847022\t100.481153847022\t0\t0\t0\tNA\t0\t0\n-mz_100.501252087615\t100.501252087615\t0\t0\t0\tNA\t0\t0\n-mz_100.521354348259\t100.521354348259\t0\t0\t0\tNA\t0\t0\n-mz_100.541460629757\t100.541460629757\t0\t0\t0\tNA\t0\t0\n-mz_100.561570932913\t100.561570932913\t0\t0\t0\tNA\t0\t0\n-mz_100.581685258532\t100.581685258532\t0.00161491779403554\t0\t0.00484475338210662\t300\t0.0145342601463199\t1\n-mz_100.601803607419\t100.601803607419\t0\t0\t0\tNA\t0\t0\n-mz_100.621925980377\t100.621925980377\t0\t0\t0\tNA\t0\t0\n-mz_100.642052378213\t100.642052378213\t0\t0\t0\tNA\t0\t0\n-mz_100.662182801731\t100.662182801731\t0.0295970870388879\t0\t0.0887912611166636\t300\t0.266373783349991\t1\n-mz_100.682317251737\t100.682317251737\t0\t0\t0\tNA\t0\t0\n-mz_100.702455729035\t100.702455729035\t0\t0\t0\tNA\t0\t0\n-mz_100.722598234431\t100.722598234431\t0\t0\t0\tNA\t0\t0\n-mz_100.742744768731\t100.742744768731\t0.027905543645223\t0\t0.0837166309356689\t300\t0.251149892807007\t1\n-mz_100.762895332742\t100.762895332742\t0\t0\t0\tNA\t0\t0\n-mz_100.783049927268\t100.783049927268\t0\t0\t0\tNA\t0\t0\n-mz_100.803208553116\t100.803208553116\t0\t0\t0\tNA\t0\t0\n-mz_100.823371211092\t100.823371211092\t0.0083441242782606\t0\t0.0201507346585991\t241.496099370175\t0.0750971185043454\t2\n-mz_100.843537902003\t100.843537902003\t0\t0\t0\tNA\t0\t0\n-mz_100.863708626656\t100.863708626656\t0\t0\t0\tNA\t0\t0\n-mz_100.883883385858\t100.883883385858\t0\t0\t0\tNA\t0\t0\n-mz_100.904062180414\t100.904062180414\t0\t0\t0\tNA\t0\t0\n-mz_100.924245011133\t100.924245011133\t0.0367837401055214\t0\t0.0819494717398366\t222.787219311436\t0.331053660949692\t3\n-mz_100.944431878822\t100.944431878822\t0\t0\t0\tNA\t0\t0\n-mz_100.964622784289\t100.964622784289\t0\t0\t0\tNA\t0\t0\n-mz_100.98481772834\t100.98481772834\t0\t0\t0\tNA\t0\t0\n-mz_101.005016711784\t101.005016711784\t0.062111565636264\t0\t0.118073778962174\t190.099505225217\t0.559004090726376\t3\n-mz_101.025219735429\t101.025219735429\t0\t0\t0\tNA\t0\t0\n-mz_101.045426800082\t101.045426800082\t0\t0\t0\tNA\t0\t0\n-mz_101.065637906553\t101.065637906553\t0\t0\t0\tNA\t0\t0\n-mz_101.085853055649\t101.085853055649\t0.125321019026968\t0\t0.229086966323655\t182.800114539731\t1.12788917124271\t3\n-mz_101.106072248179\t101.106072248179\t0\t0\t0\tNA\t0\t0\n-mz_101.126295484953\t101.126295484953\t0\t0\t0\tNA\t0\t0\n-mz_101.146522766778\t101.146522766778\t0\t0\t0\tNA\t0\t0\n-mz_101.166754094464\t101.166754094464\t0.110433474390043\t0\t0.241764556418413\t218.923254704925\t0.993901269510388\t3\n-mz_101.18698946882\t101.18698946882\t0\t0\t0\tNA\t0\t0\n-mz_101.207228890656\t101.207228890656\t0\t0\t0\tNA\t0\t0\n-mz_101.227472360782\t101.227472360782\t0\t0\t0\tNA\t0\t0\n-mz_101.247719880006\t101.247719880006\t0.0220825859572263\t0\t0.0489671939640457\t221.745741458426\t0.198743273615037\t3\n-mz_101.267971449139\t101.267971449139\t0\t0\t0\tNA\t0\t0\n-mz_101.28822706899\t101.28822706899\t0\t0\t0\tNA\t0\t0\n-mz_101.308486740371\t101.308486740371\t0\t0\t0\tNA\t0\t0\n-mz_101.328750464092\t101.328750464092'..b'\t0.109568835592831\t292.414989166609\t0.337232890538871\t2\n-mz_794.704377181409\t794.704377181409\t0.15831301940812\t1.39839147066058e-38\t0.342155960501196\t216.126230034904\t1.42481717467308\t5\n-mz_794.863333952522\t794.863333952522\t0.061700455553364\t2.09150662162954e-38\t0.147614505083265\t239.243784765243\t0.555304099980276\t6\n-mz_795.022322518169\t795.022322518169\t0.0108078516398867\t0\t0.0324235549196601\t300\t0.0972706647589803\t1\n-mz_795.18134288471\t795.18134288471\t1.03806936143277e-05\t0\t2.06207299669125e-05\t198.645010950437\t9.34262425289489e-05\t3\n-mz_795.340395058504\t795.340395058504\t4.27814623233442e-06\t0\t8.1280368419713e-06\t189.989691809486\t3.85033160910098e-05\t4\n-mz_795.499479045915\t795.499479045915\t1.34739204642958e-06\t0\t4.04217613928874e-06\t300\t1.21265284178662e-05\t1\n-mz_795.658594853305\t795.658594853305\t2.41733044100319e-07\t0\t7.24443858335399e-07\t299.687558658615\t2.17559739690287e-06\t3\n-mz_795.817742487039\t795.817742487039\t6.82981933354378e-10\t0\t1.46305214500577e-09\t214.215350883467\t6.1468374001894e-09\t3\n-mz_795.976921953483\t795.976921953483\t1.97925830865682e-10\t0\t4.47965241832071e-10\t226.329852891245\t1.78133247779114e-09\t3\n-mz_796.136133259004\t796.136133259004\t4.59929004603676e-11\t0\t1.37978701381103e-10\t300\t4.13936104143309e-10\t1\n-mz_796.295376409971\t796.295376409971\t4.93382472915889e-14\t0\t9.79336915953797e-14\t198.494468229874\t4.440442256243e-13\t3\n-mz_796.454651412753\t796.454651412753\t2.04924542989995e-14\t0\t3.94621959061835e-14\t192.56939813261\t1.84432088690996e-13\t3\n-mz_796.613958273722\t796.613958273722\t0.0640500783920358\t0\t0.192150235176084\t299.999999999963\t0.576450705528322\t2\n-mz_796.773296999249\t796.773296999249\t0.0406853891909122\t0\t0.122056167572737\t300\t0.36616850271821\t3\n-mz_796.932667595709\t796.932667595709\t1.45479372341066e-18\t0\t3.89552090887857e-18\t267.771357972718\t1.30931435106959e-17\t2\n-mz_797.092070069475\t797.092070069475\t3.53827797679273e-07\t0\t1.06148339303488e-06\t299.99999999917\t3.18445017911345e-06\t2\n-mz_797.251504426925\t797.251504426925\t4.13144920862074e-06\t0\t1.23943476258622e-05\t299.999999999999\t3.71830428775867e-05\t2\n-mz_797.410970674435\t797.410970674435\t1.09320730403953e-06\t0\t3.27962191211858e-06\t300\t9.83886573635573e-06\t3\n-mz_797.570468818384\t797.570468818384\t9.69305316816355e-23\t0\t1.9109331645976e-22\t197.144607735567\t8.7237478513472e-22\t3\n-mz_797.729998865153\t797.729998865153\t3.54466308157491e-10\t0\t1.06339892447237e-09\t299.999999999971\t3.19019677341742e-09\t2\n-mz_797.889560821122\t797.889560821122\t0.0289176803618284\t0\t0.086753040485471\t299.999997925095\t0.260259123256456\t3\n-mz_798.049154692673\t798.049154692673\t0.0374488714668486\t0\t0.112346614400546\t300\t0.337039843201637\t3\n-mz_798.208780486191\t798.208780486191\t0.000266989253263465\t0\t0.000800967759759802\t299.999999988541\t0.00240290327937119\t3\n-mz_798.368438208061\t798.368438208061\t2.34458102407087e-14\t0\t7.0337430722126e-14\t299.999999999999\t2.11012292166378e-13\t2\n-mz_798.528127864668\t798.528127864668\t0.00141713557604831\t0\t0.0042384206336443\t299.083637817008\t0.0127542201844348\t4\n-mz_798.687849462401\t798.687849462401\t0.181158882302081\t0\t0.543476171075702\t299.999737340761\t1.63042994071873\t4\n-mz_798.847603007648\t798.847603007648\t0.0144867946704229\t0\t0.0434603840112686\t300\t0.130381152033806\t3\n-mz_799.007388506799\t799.007388506799\t2.4237529276071e-10\t0\t7.27125877994982e-10\t299.999999881527\t2.18137763484639e-09\t3\n-mz_799.167205966246\t799.167205966246\t3.01763521578143e-11\t0\t9.05290564734429e-11\t300\t2.71587169420329e-10\t3\n-mz_799.327055392382\t799.327055392382\t1.10960895597907e-05\t0\t3.32882668224669e-05\t299.999983265229\t9.98648060381163e-05\t4\n-mz_799.486936791601\t799.486936791601\t2.06164372684725e-07\t0\t6.18493118054175e-07\t300\t1.85547935416253e-06\t3\n-mz_799.646850170297\t799.646850170297\t0.051657970580808\t0\t0.154973911742362\t299.999999999881\t0.464921735227272\t4\n-mz_799.806795534868\t799.806795534868\t0.0394212479392693\t0\t0.118263743817806\t299.999999999995\t0.354791231453424\t2\n-mz_799.96677289171\t799.96677289171\t8.54203856374182e-27\t0\t2.56261156912255e-26\t300\t7.68783470736764e-26\t1\n' |
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/features_test2.tabular --- a/test-data/features_test2.tabular Wed Apr 19 22:52:19 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,8155 +0,0 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|
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/features_test4.tabular --- a/test-data/features_test4.tabular Wed Apr 19 22:52:19 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,8155 +0,0 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|
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/features_test6.tabular --- a/test-data/features_test6.tabular Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/features_test6.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
| b'@@ -1,8155 +1,21 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|
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/features_test7.tabular --- a/test-data/features_test7.tabular Wed Apr 19 22:52:19 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,8155 +0,0 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| diff -r bb6397b94018 -r 56da27be956a test-data/loadings_and_weights_test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/loadings_and_weights_test2.tabular Thu Jul 04 13:34:08 2024 +0000 |
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|
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/loadings_and_weights_test4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/loadings_and_weights_test4.tabular Thu Jul 04 13:34:08 2024 +0000 |
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| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/loadings_and_weights_test7.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/loadings_and_weights_test7.tabular Thu Jul 04 13:34:08 2024 +0000 |
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|
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| diff -r bb6397b94018 -r 56da27be956a test-data/out8.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.html Thu Jul 04 13:34:08 2024 +0000 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 256 +-rw-r--r-- 1 maren maren 248824 Jun 18 14:22 ibd +-rw-r--r-- 1 maren maren 12071 Jun 18 14:22 imzml |
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| diff -r bb6397b94018 -r 56da27be956a test-data/out8.ibd |
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| Binary file test-data/out8.ibd has changed |
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/out8.imzml --- a/test-data/out8.imzml Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/out8.imzml Thu Jul 04 13:34:08 2024 +0000 |
| b |
| @@ -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="02059ae7-7beb-4ecf-92ae-7a767e04bf43" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="dc3960918fa3008824889b4ac142be1d0534ded8" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="fec96ef3-8c76-4add-ad75-63cb9f271dd3" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9dc25cdfbad3d0e23313616b35c0e5a7667e0934" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,16 +42,12 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.6.0"> + <software id="Cardinal" version="3.4.3"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> - <cvParam cvRef="IMS" accession="IMS:1000401" name="top down" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right" value="" /> <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" /> |
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| diff -r bb6397b94018 -r 56da27be956a test-data/pixel_out4.tabular --- a/test-data/pixel_out4.tabular Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/pixel_out4.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
| @@ -1,10 +1,10 @@ spectra_names x_values y_values pixel_order peaks_per_spectrum median_intensity spectrum_TIC maximum_intensity most_abundant_mz mz_count -xy_1_1 1 1 1 1662 0 121.85 3.05 152.928453433486 7 -xy_2_1 2 1 2 2512 0 182.32 4.76 153.081458377151 8 -xy_3_1 3 1 3 2523 0 161.81 3.48 152.989637050972 17 -xy_1_2 1 2 4 2508 0 200.96 4.6 153.081458377151 16 -xy_2_2 2 2 5 2273 0 135.31 2.38 328.905406095478 10 -xy_3_2 3 2 6 1908 0 108.4 1.97 171.257828125883 9 -xy_1_3 1 3 7 2160 0 127.85 2.27 153.173334812658 8 -xy_2_3 2 3 8 2523 0 168.27 3.83 152.989637050972 15 -xy_3_3 3 3 9 2788 0 243.54 9.24 153.081458377151 8 +xy_1_1 1 1 1 2566 0 189.35 3.05 152.897870801063 11 +xy_2_1 2 1 2 3747 0 247.76 4.76 153.081458377151 8 +xy_3_1 3 1 3 3666 0 212.81 3.48 152.989637050972 19 +xy_1_2 1 2 4 3668 0 272.52 4.6 153.081458377151 19 +xy_2_2 2 2 5 3348 0 177.37 2.38 328.905406095478 10 +xy_3_2 3 2 6 2803 0 146.22 1.97 171.223579985072 9 +xy_1_3 1 3 7 3241 0 174 2.27 153.142703208856 8 +xy_2_3 2 3 8 3723 0 227.73 3.83 152.989637050972 16 +xy_3_3 3 3 9 4070 0 334.59 9.24 153.081458377151 8 |
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| diff -r bb6397b94018 -r 56da27be956a test-data/pixels_test2.tabular --- a/test-data/pixels_test2.tabular Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/pixels_test2.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
| @@ -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 A -xy_4_1 4 1 A -xy_1_2 1 2 B -xy_2_2 2 2 B -xy_3_2 3 2 B -xy_4_2 4 2 B -xy_1_3 1 3 C -xy_2_3 2 3 C -xy_3_3 3 3 C -xy_4_3 4 3 C -xy_10_1 10 1 A -xy_11_1 11 1 A -xy_12_1 12 1 A -xy_13_1 13 1 A -xy_10_2 10 2 B -xy_11_2 11 2 B -xy_12_2 12 2 B -xy_13_2 13 2 B -xy_10_3 10 3 B -xy_11_3 11 3 C -xy_12_3 12 3 C -xy_13_3 13 3 C +pixel_name x y predicted_class annotated_class correct +xy_1_1 1 1 A A TRUE +xy_2_1 2 1 A A TRUE +xy_3_1 3 1 A A TRUE +xy_4_1 4 1 A A TRUE +xy_1_2 1 2 B B TRUE +xy_2_2 2 2 B B TRUE +xy_3_2 3 2 B B TRUE +xy_4_2 4 2 C B FALSE +xy_1_3 1 3 C C TRUE +xy_2_3 2 3 C C TRUE +xy_3_3 3 3 C C TRUE +xy_4_3 4 3 C C TRUE +xy_10_1 10 1 A A TRUE +xy_11_1 11 1 A A TRUE +xy_12_1 12 1 B A FALSE +xy_13_1 13 1 A A TRUE +xy_10_2 10 2 B B TRUE +xy_11_2 11 2 B B TRUE +xy_12_2 12 2 B B TRUE +xy_13_2 13 2 B B TRUE +xy_10_3 10 3 B C FALSE +xy_11_3 11 3 B C FALSE +xy_12_3 12 3 C C TRUE +xy_13_3 13 3 B C FALSE |
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/pixels_test4.tabular --- a/test-data/pixels_test4.tabular Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/pixels_test4.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
| @@ -1,25 +1,25 @@ -pixel names x y predicted condition -xy_1_1 1 1 A -xy_2_1 2 1 C -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 B -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 A -xy_11_1 11 1 C -xy_12_1 12 1 C -xy_13_1 13 1 B -xy_10_2 10 2 B -xy_11_2 11 2 A -xy_12_2 12 2 C -xy_13_2 13 2 A -xy_10_3 10 3 C -xy_11_3 11 3 B -xy_12_3 12 3 B -xy_13_3 13 3 C +pixel names x y predicted_class annotated_class correct +xy_1_1 1 1 C A FALSE +xy_2_1 2 1 C A FALSE +xy_3_1 3 1 B B TRUE +xy_4_1 4 1 C C TRUE +xy_1_2 1 2 C C TRUE +xy_2_2 2 2 C C TRUE +xy_3_2 3 2 B B TRUE +xy_4_2 4 2 C A FALSE +xy_1_3 1 3 C A FALSE +xy_2_3 2 3 B B TRUE +xy_3_3 3 3 C C TRUE +xy_4_3 4 3 C A FALSE +xy_10_1 10 1 B A FALSE +xy_11_1 11 1 C C TRUE +xy_12_1 12 1 B B TRUE +xy_13_1 13 1 B B TRUE +xy_10_2 10 2 B B TRUE +xy_11_2 11 2 B A FALSE +xy_12_2 12 2 C C TRUE +xy_13_2 13 2 B A FALSE +xy_10_3 10 3 C C TRUE +xy_11_3 11 3 B B TRUE +xy_12_3 12 3 B B TRUE +xy_13_3 13 3 C C TRUE |
| b |
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| b |
| b'@@ -1,211 +1,211 @@\n x\ty\tpixel_names\tclass\tX1\tX2\tX3\tX4\tX5\n-1\t1\txy_1_1\t2\t0.103020335449098\t0.896979664550903\tNA\tNA\tNA\n-2\t1\txy_2_1\t2\t0.105473181113881\t0.894526818886119\tNA\tNA\tNA\n-3\t1\txy_3_1\t3\tNA\tNA\t0.875615363102476\t0.124384636897524\tNA\n-4\t1\txy_4_1\t3\tNA\tNA\t0.851266299854111\t0.148733700145889\tNA\n-5\t1\txy_5_1\t3\tNA\tNA\t0.860051638085976\t0.139948361914025\tNA\n-6\t1\txy_6_1\t3\tNA\tNA\t0.761647436676139\t0.238352563323861\tNA\n-7\t1\txy_7_1\t2\t0.182529426057793\t0.817470573942208\tNA\tNA\tNA\n-8\t1\txy_8_1\t1\t0.941039895576799\t0.0589601044232009\tNA\tNA\tNA\n-9\t1\txy_9_1\t1\t0.943908265739545\t0.0560917342604552\tNA\tNA\tNA\n-10\t1\txy_10_1\t1\t0.946144146674231\t0.0538558533257694\tNA\tNA\tNA\n-11\t1\txy_11_1\t1\t0.946407758474576\t0.0535922415254241\tNA\tNA\tNA\n-12\t1\txy_12_1\t1\t0.954188476238198\t0.0458115237618019\tNA\tNA\tNA\n-13\t1\txy_13_1\t1\t0.946620679361554\t0.0533793206384464\tNA\tNA\tNA\n-14\t1\txy_14_1\t1\t0.946383603328925\t0.0536163966710746\tNA\tNA\tNA\n-15\t1\txy_15_1\t1\t0.954534262297142\t0.0454657377028575\tNA\tNA\tNA\n-16\t1\txy_16_1\t1\t0.946937989073607\t0.053062010926393\tNA\tNA\tNA\n-17\t1\txy_17_1\t1\t0.947433161876214\t0.0525668381237858\tNA\tNA\tNA\n-18\t1\txy_18_1\t1\t0.947739055467613\t0.0522609445323874\tNA\tNA\tNA\n-19\t1\txy_19_1\t1\t0.947751293668412\t0.0522487063315876\tNA\tNA\tNA\n-20\t1\txy_20_1\t1\t0.952255848236646\t0.0477441517633543\tNA\tNA\tNA\n-1\t2\txy_1_2\t3\tNA\tNA\t0.859206228983602\t0.140793771016398\tNA\n-2\t2\txy_2_2\t3\tNA\tNA\t0.868966809797105\t0.131033190202895\tNA\n-3\t2\txy_3_2\t3\tNA\tNA\t0.875160479466722\t0.124839520533278\tNA\n-4\t2\txy_4_2\t3\tNA\tNA\t0.804220530331249\t0.195779469668752\tNA\n-5\t2\txy_5_2\t3\tNA\tNA\t0.794510153832606\t0.205489846167394\tNA\n-6\t2\txy_6_2\t3\tNA\tNA\t0.856628649807154\t0.143371350192846\tNA\n-7\t2\txy_7_2\t3\tNA\tNA\t0.855718253316932\t0.144281746683068\tNA\n-8\t2\txy_8_2\t3\tNA\tNA\t0.827753889743415\t0.172246110256585\tNA\n-9\t2\txy_9_2\t1\t0.946284298320806\t0.0537157016791942\tNA\tNA\tNA\n-10\t2\txy_10_2\t1\t0.769374657306886\t0.230625342693115\tNA\tNA\tNA\n-11\t2\txy_11_2\t1\t0.945090766923877\t0.0549092330761232\tNA\tNA\tNA\n-12\t2\txy_12_2\t1\t0.945737335422033\t0.054262664577967\tNA\tNA\tNA\n-13\t2\txy_13_2\t1\t0.945600558567459\t0.0543994414325411\tNA\tNA\tNA\n-14\t2\txy_14_2\t1\t0.950847256021339\t0.0491527439786609\tNA\tNA\tNA\n-15\t2\txy_15_2\t1\t0.945219115579397\t0.0547808844206027\tNA\tNA\tNA\n-16\t2\txy_16_2\t1\t0.94620821674802\t0.0537917832519801\tNA\tNA\tNA\n-17\t2\txy_17_2\t1\t0.953530272335786\t0.0464697276642139\tNA\tNA\tNA\n-18\t2\txy_18_2\t1\t0.951570612821144\t0.0484293871788565\tNA\tNA\tNA\n-19\t2\txy_19_2\t1\t0.955821461571265\t0.0441785384287349\tNA\tNA\tNA\n-20\t2\txy_20_2\t1\t0.947743776276186\t0.0522562237238136\tNA\tNA\tNA\n-1\t3\txy_1_3\t3\tNA\tNA\t0.835481115700174\t0.164518884299826\tNA\n-2\t3\txy_2_3\t3\tNA\tNA\t0.695409629420474\t0.304590370579526\tNA\n-3\t3\txy_3_3\t3\tNA\tNA\t0.876462568112197\t0.123537431887803\tNA\n-4\t3\txy_4_3\t3\tNA\tNA\t0.85082264789337\t0.14917735210663\tNA\n-5\t3\txy_5_3\t3\tNA\tNA\t0.878890510088586\t0.121109489911414\tNA\n-6\t3\txy_6_3\t3\tNA\tNA\t0.870311243843917\t0.129688756156083\tNA\n-7\t3\txy_7_3\t3\tNA\tNA\t0.87300813797666\t0.12699186202334\tNA\n-8\t3\txy_8_3\t3\tNA\tNA\t0.811661586530175\t0.188338413469825\tNA\n-9\t3\txy_9_3\t3\tNA\tNA\t0.856157399446096\t0.143842600553904\tNA\n-10\t3\txy_10_3\t1\t0.865627377090542\t0.134372622909458\tNA\tNA\tNA\n-11\t3\txy_11_3\t1\t0.94682656889567\t0.0531734311043297\tNA\tNA\tNA\n-12\t3\txy_12_3\t1\t0.893467278448154\t0.106532721551846\tNA\tNA\tNA\n-13\t3\txy_13_3\t1\t0.664961582397203\t0.335038417602797\tNA\tNA\tNA\n-14\t3\txy_14_3\t1\t0.944081001351204\t0.0559189986487956\tNA\tNA\tNA\n-15\t3\txy_15_3\t2\t0.490705121594534\t0.509294878405466\tNA\tNA\tNA\n-16\t3\txy_16_3\t1\t0.945709649905103\t0.054290350094897\tNA\tNA\tNA\n-17\t3\txy_17_3\t1\t0.954438913225744\t0.0455610867742563\tNA\tNA\tNA\n-18\t3\txy_18_3\t1\t0.947733594972515\t0.0522664050274855\tNA\tNA\tNA\n-19\t3\txy_19_3\t1\t0.940190235235463\t0.0598097647645374\tNA\tNA\tNA\n-20\t3\txy_20_3\t1\t0.947744927295705\t0.0522550727042953\tNA\tNA\tNA\n-1\t4\txy_1_4\t3\tNA\tNA\t0.859290347356755\t0.140709652643245\tNA\n-2\t4\txy_2_4\t3\tNA\tNA\t0.848944520847906\t0.151055479152094\tNA\n-3\t4\txy_3_4\t3\tNA\tNA\t0.862233623147597\t0.137766376852403\tNA\n-4\t4\txy_4_4\t3\tNA\tNA\t0.877889844474806\t0.122110155525194\tNA\n-5\t4\txy_5_4\t3\tNA\tNA\t0.832791852661168\t0.167208147338832\tNA\n-6\t4\txy_6_4\t3\tNA\tN'..b'992\tNA\tNA\tNA\n-4\t17\txy_4_17\t1\t0.952616455037497\t0.0473835449625028\tNA\tNA\tNA\n-5\t17\txy_5_17\t1\t0.952145463899211\t0.0478545361007892\tNA\tNA\tNA\n-6\t17\txy_6_17\t1\t0.949486664118868\t0.0505133358811326\tNA\tNA\tNA\n-7\t17\txy_7_17\t1\t0.955041365581388\t0.0449586344186117\tNA\tNA\tNA\n+1\t17\txy_1_17\t1\t0.948669450786587\t0.0513305492134131\tNA\tNA\tNA\n+2\t17\txy_2_17\t1\t0.944598570307394\t0.0554014296926063\tNA\tNA\tNA\n+3\t17\txy_3_17\t1\t0.809340578213783\t0.190659421786217\tNA\tNA\tNA\n+4\t17\txy_4_17\t1\t0.951579194451817\t0.0484208055481834\tNA\tNA\tNA\n+5\t17\txy_5_17\t1\t0.950780622028483\t0.049219377971517\tNA\tNA\tNA\n+6\t17\txy_6_17\t1\t0.947554332341236\t0.052445667658764\tNA\tNA\tNA\n+7\t17\txy_7_17\t1\t0.95428917887965\t0.0457108211203498\tNA\tNA\tNA\n 8\t17\txy_8_17\t5\tNA\tNA\tNA\tNA\t1\n 9\t17\txy_9_17\t5\tNA\tNA\tNA\tNA\t1\n 10\t17\txy_10_17\t5\tNA\tNA\tNA\tNA\t1\n@@ -339,13 +339,13 @@\n 18\t17\txy_18_17\t5\tNA\tNA\tNA\tNA\t1\n 19\t17\txy_19_17\t5\tNA\tNA\tNA\tNA\t1\n 20\t17\txy_20_17\t5\tNA\tNA\tNA\tNA\t1\n-1\t18\txy_1_18\t1\t0.924283612907066\t0.0757163870929339\tNA\tNA\tNA\n-2\t18\txy_2_18\t1\t0.833271075296862\t0.166728924703139\tNA\tNA\tNA\n-3\t18\txy_3_18\t1\t0.950506749170232\t0.0494932508297682\tNA\tNA\tNA\n-4\t18\txy_4_18\t1\t0.945030112956943\t0.054969887043057\tNA\tNA\tNA\n-5\t18\txy_5_18\t1\t0.947419130420145\t0.0525808695798547\tNA\tNA\tNA\n-6\t18\txy_6_18\t1\t0.94636686386672\t0.0536331361332798\tNA\tNA\tNA\n-7\t18\txy_7_18\t1\t0.946842051526658\t0.0531579484733416\tNA\tNA\tNA\n+1\t18\txy_1_18\t1\t0.92890386876909\t0.07109613123091\tNA\tNA\tNA\n+2\t18\txy_2_18\t1\t0.846646361169419\t0.153353638830581\tNA\tNA\tNA\n+3\t18\txy_3_18\t1\t0.949406991975157\t0.0505930080248429\tNA\tNA\tNA\n+4\t18\txy_4_18\t1\t0.942726194486836\t0.0572738055131639\tNA\tNA\tNA\n+5\t18\txy_5_18\t1\t0.945294862227375\t0.0547051377726251\tNA\tNA\tNA\n+6\t18\txy_6_18\t1\t0.944030047296127\t0.0559699527038728\tNA\tNA\tNA\n+7\t18\txy_7_18\t1\t0.944663148584212\t0.0553368514157875\tNA\tNA\tNA\n 8\t18\txy_8_18\t5\tNA\tNA\tNA\tNA\t1\n 9\t18\txy_9_18\t5\tNA\tNA\tNA\tNA\t1\n 10\t18\txy_10_18\t5\tNA\tNA\tNA\tNA\t1\n@@ -359,13 +359,13 @@\n 18\t18\txy_18_18\t5\tNA\tNA\tNA\tNA\t1\n 19\t18\txy_19_18\t5\tNA\tNA\tNA\tNA\t1\n 20\t18\txy_20_18\t5\tNA\tNA\tNA\tNA\t1\n-1\t19\txy_1_19\t1\t0.945469095167889\t0.0545309048321114\tNA\tNA\tNA\n-2\t19\txy_2_19\t1\t0.947686502636905\t0.052313497363095\tNA\tNA\tNA\n-3\t19\txy_3_19\t1\t0.500724657394895\t0.499275342605105\tNA\tNA\tNA\n-4\t19\txy_4_19\t1\t0.943283865302304\t0.0567161346976964\tNA\tNA\tNA\n-5\t19\txy_5_19\t1\t0.943587862592802\t0.0564121374071975\tNA\tNA\tNA\n-6\t19\txy_6_19\t1\t0.943792124413294\t0.0562078755867061\tNA\tNA\tNA\n-7\t19\txy_7_19\t1\t0.923971584962464\t0.0760284150375363\tNA\tNA\tNA\n+1\t19\txy_1_19\t1\t0.943344108721234\t0.0566558912787659\tNA\tNA\tNA\n+2\t19\txy_2_19\t1\t0.946066689819065\t0.0539333101809345\tNA\tNA\tNA\n+3\t19\txy_3_19\t1\t0.500841511070196\t0.499158488929804\tNA\tNA\tNA\n+4\t19\txy_4_19\t1\t0.940738021656634\t0.0592619783433659\tNA\tNA\tNA\n+5\t19\txy_5_19\t1\t0.940922080362541\t0.0590779196374587\tNA\tNA\tNA\n+6\t19\txy_6_19\t1\t0.94120183822192\t0.0587981617780802\tNA\tNA\tNA\n+7\t19\txy_7_19\t1\t0.928058102608011\t0.0719418973919887\tNA\tNA\tNA\n 8\t19\txy_8_19\t5\tNA\tNA\tNA\tNA\t1\n 9\t19\txy_9_19\t5\tNA\tNA\tNA\tNA\t1\n 10\t19\txy_10_19\t5\tNA\tNA\tNA\tNA\t1\n@@ -379,13 +379,13 @@\n 18\t19\txy_18_19\t5\tNA\tNA\tNA\tNA\t1\n 19\t19\txy_19_19\t5\tNA\tNA\tNA\tNA\t1\n 20\t19\txy_20_19\t5\tNA\tNA\tNA\tNA\t1\n-1\t20\txy_1_20\t1\t0.945806686367799\t0.054193313632201\tNA\tNA\tNA\n-2\t20\txy_2_20\t1\t0.916303384573456\t0.0836966154265443\tNA\tNA\tNA\n-3\t20\txy_3_20\t1\t0.951763565776223\t0.0482364342237765\tNA\tNA\tNA\n-4\t20\txy_4_20\t1\t0.943923476961385\t0.0560765230386148\tNA\tNA\tNA\n-5\t20\txy_5_20\t2\t0.425906202005294\t0.574093797994706\tNA\tNA\tNA\n-6\t20\txy_6_20\t1\t0.940077538712559\t0.0599224612874413\tNA\tNA\tNA\n-7\t20\txy_7_20\t2\t0.499816861759627\t0.500183138240373\tNA\tNA\tNA\n+1\t20\txy_1_20\t1\t0.943650404283968\t0.0563495957160318\tNA\tNA\tNA\n+2\t20\txy_2_20\t1\t0.92162589138458\t0.0783741086154201\tNA\tNA\tNA\n+3\t20\txy_3_20\t1\t0.951746780075924\t0.0482532199240765\tNA\tNA\tNA\n+4\t20\txy_4_20\t1\t0.941434992979074\t0.0585650070209257\tNA\tNA\tNA\n+5\t20\txy_5_20\t2\t0.366042261623588\t0.633957738376412\tNA\tNA\tNA\n+6\t20\txy_6_20\t1\t0.937081048926282\t0.062918951073718\tNA\tNA\tNA\n+7\t20\txy_7_20\t2\t0.498954835693212\t0.501045164306788\tNA\tNA\tNA\n 8\t20\txy_8_20\t5\tNA\tNA\tNA\tNA\t1\n 9\t20\txy_9_20\t5\tNA\tNA\tNA\tNA\t1\n 10\t20\txy_10_20\t5\tNA\tNA\tNA\tNA\t1\n' |
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| diff -r bb6397b94018 -r 56da27be956a test-data/toplabels_proc.tabular --- a/test-data/toplabels_proc.tabular Wed Apr 19 22:52:19 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,101 +0,0 @@ -mz r k s classes centers tstatistics p.values adj.p.values -1199 1 2 0 1 0 0 1 1 -1200 1 2 0 1 3.06556174490187 0 1 1 -1201 1 2 0 1 1.24045880635579 0 1 1 -1202 1 2 0 1 0.269693666034275 0 1 1 -1203 1 2 0 1 0 0 1 1 -1204 1 2 0 1 0 0 1 1 -1205 1 2 0 1 0 0 1 1 -1206 1 2 0 1 0 0 1 1 -1207 1 2 0 1 0 0 1 1 -1208 1 2 0 1 0 0 1 1 -1209 1 2 0 1 1.43794178962708 0 1 1 -1210 1 2 0 1 0.82622406217787 0 1 1 -1211 1 2 0 1 0.249723381466336 0 1 1 -1212 1 2 0 1 0 0 1 1 -1213 1 2 0 1 0 0 1 1 -1214 1 2 0 1 0.247201071845161 0 1 1 -1215 1 2 0 1 0.517291307449341 0 1 1 -1216 1 2 0 1 0 0 1 1 -1217 1 2 0 1 0 0 1 1 -1218 1 2 0 1 0 0 1 1 -1219 1 2 0 1 0 0 1 1 -1220 1 2 0 1 0.278993447621663 0 1 1 -1221 1 2 0 1 0 0 1 1 -1222 1 2 0 1 0.241794321272108 0 1 1 -1223 1 2 0 1 1.01245986090766 0 1 1 -1224 1 2 0 1 0.803900904125638 0 1 1 -1225 1 2 0 1 0.456217077043321 0 1 1 -1226 1 2 0 1 0 0 1 1 -1227 1 2 0 1 0 0 1 1 -1228 1 2 0 1 0 0 1 1 -1229 1 2 0 1 0 0 1 1 -1230 1 2 0 1 0 0 1 1 -1231 1 2 0 1 0 0 1 1 -1232 1 2 0 1 0 0 1 1 -1233 1 2 0 1 0 0 1 1 -1234 1 2 0 1 0 0 1 1 -1235 1 2 0 1 0 0 1 1 -1236 1 2 0 1 0 0 1 1 -1237 1 2 0 1 0 0 1 1 -1238 1 2 0 1 0 0 1 1 -1239 1 2 0 1 0 0 1 1 -1240 1 2 0 1 0.517177846696642 0 1 1 -1241 1 2 0 1 0 0 1 1 -1242 1 2 0 1 0 0 1 1 -1243 1 2 0 1 0 0 1 1 -1244 1 2 0 1 0.220909158388774 0 1 1 -1245 1 2 0 1 0.441907816463047 0 1 1 -1246 1 2 0 1 0 0 1 1 -1247 1 2 0 1 0 0 1 1 -1248 1 2 0 1 0 0 1 1 -1249 1 2 0 1 0 0 1 1 -1250 1 2 0 1 0 0 1 1 -1251 1 2 0 1 0 0 1 1 -1252 1 2 0 1 0 0 1 1 -1253 1 2 0 1 0 0 1 1 -1254 1 2 0 1 0 0 1 1 -1255 1 2 0 1 0 0 1 1 -1256 1 2 0 1 0 0 1 1 -1257 1 2 0 1 0 0 1 1 -1258 1 2 0 1 0 0 1 1 -1259 1 2 0 1 0 0 1 1 -1260 1 2 0 1 0 0 1 1 -1261 1 2 0 1 0.32789675394694 0 1 1 -1262 1 2 0 1 0.268932872348362 0 1 1 -1263 1 2 0 1 0 0 1 1 -1264 1 2 0 1 2.64317909876506 0 1 1 -1265 1 2 0 1 1.4933132065667 0 1 1 -1266 1 2 0 1 0 0 1 1 -1267 1 2 0 1 0.584092458089193 0 1 1 -1268 1 2 0 1 2.51373351944817 0 1 1 -1269 1 2 0 1 1.80340676837497 0 1 1 -1270 1 2 0 1 0 0 1 1 -1271 1 2 0 1 0 0 1 1 -1272 1 2 0 1 0 0 1 1 -1273 1 2 0 1 0 0 1 1 -1274 1 2 0 1 0 0 1 1 -1275 1 2 0 1 0 0 1 1 -1276 1 2 0 1 0 0 1 1 -1277 1 2 0 1 0 0 1 1 -1278 1 2 0 1 0 0 1 1 -1279 1 2 0 1 0 0 1 1 -1280 1 2 0 1 0 0 1 1 -1281 1 2 0 1 0.250744581222534 0 1 1 -1282 1 2 0 1 0.760214355256822 0 1 1 -1283 1 2 0 1 0 0 1 1 -1284 1 2 0 1 0 0 1 1 -1285 1 2 0 1 0 0 1 1 -1286 1 2 0 1 0 0 1 1 -1287 1 2 0 1 0.238297859827677 0 1 1 -1288 1 2 0 1 0 0 1 1 -1289 1 2 0 1 1.15708703464932 0 1 1 -1290 1 2 0 1 1.00530293252733 0 1 1 -1291 1 2 0 1 0.249645392100016 0 1 1 -1292 1 2 0 1 0 0 1 1 -1293 1 2 0 1 0 0 1 1 -1294 1 2 0 1 0 0 1 1 -1295 1 2 0 1 0 0 1 1 -1296 1 2 0 1 0.231536282433404 0 1 1 -1297 1 2 0 1 2.14849718411764 0 1 1 -1298 1 2 0 1 0.742050197389391 0 1 1 |
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/toplabels_skm.tabular --- a/test-data/toplabels_skm.tabular Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/toplabels_skm.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
| @@ -1,21 +1,21 @@ -mz r k cluster centers withinss betweenss -329.083343505859 1 3 1 0.708310013016065 0 3.15454318073589 -329.083343505859 1 3 2 2.06111800670624 0.348399350284836 3.15454318073589 -329.083343505859 1 3 3 1.72517621517181 0.549843039511264 3.15454318073589 -329.083343505859 2 3 1 0.708310013016065 0 3.15454318073589 -329.083343505859 2 3 2 2.06111800670624 0.348399350284836 3.15454318073589 -329.083343505859 2 3 3 1.72517621517181 0.549843039511264 3.15454318073589 -329.083343505859 3 3 1 0.708310013016065 0 3.15454318073589 -329.083343505859 3 3 2 2.06111800670624 0.348399350284836 3.15454318073589 -329.083343505859 3 3 3 1.72517621517181 0.549843039511264 3.15454318073589 -329 1 3 1 0.982837170362473 0 3.09113153043007 -329 1 3 2 2.40426647663116 0.0706077629095319 3.09113153043007 -329 1 3 3 1.07743680477142 0.879613918408614 3.09113153043007 -329 2 3 1 0.982837170362473 0 3.09113153043007 -329 2 3 2 2.40426647663116 0.0706077629095319 3.09113153043007 -329 2 3 3 1.07743680477142 0.879613918408614 3.09113153043007 -329 3 3 1 0.982837170362473 0 3.09113153043007 -329 3 3 2 2.40426647663116 0.0706077629095319 3.09113153043007 -329 3 3 3 1.07743680477142 0.879613918408614 3.09113153043007 -329 1 2 1 0.996351403849466 0.887284567691734 3.08346088114695 -329 1 2 2 2.40426647663116 0.0706077629095319 3.08346088114695 +mz r k cluster centers correlation +345.333343505859 1 3 1 0.0279595106840134 0.988259301616822 +344.583343505859 1 3 2 0.300594985485077 0.943406904222217 +345.25 1 3 1 0.269687791665395 0.892582883710714 +329 1 2 2 2.14481588204702 0.881735659988952 +329 2 2 2 2.14481588204702 0.881735659988952 +329 2 3 2 2.14481588204702 0.881735659988952 +329 3 2 2 2.14481588204702 0.881735659988952 +329 3 3 2 2.14481588204702 0.881735659988952 +329 1 3 2 2.40426647663116 0.873485735155449 +345.75 1 3 1 3.58992256224155e-05 0.857818092959862 +327.083343505859 1 3 2 0.863447278738022 0.827292558345092 +333.166687011719 2 3 3 1.61538400683879e-31 0.75592893935933 +333.166687011719 3 3 3 1.61538400683879e-31 0.75592893935933 +332.083343505859 2 3 3 4.06468533133051e-23 0.755899032346127 +332.083343505859 3 3 3 4.06468533133051e-23 0.755899032346127 +331 2 3 3 1.00770013309971e-14 0.755827385161935 +331 3 3 3 1.00770013309971e-14 0.755827385161935 +346.416687011719 1 3 1 6.57087763829741e-11 0.75578217468527 +346.416687011719 2 3 3 6.57087763829741e-11 0.75578217468527 +346.416687011719 3 3 3 6.57087763829741e-11 0.75578217468527 |
| b |
| diff -r bb6397b94018 -r 56da27be956a test-data/toplabels_ssc.tabular --- a/test-data/toplabels_ssc.tabular Wed Apr 19 22:52:19 2023 +0000 +++ b/test-data/toplabels_ssc.tabular Thu Jul 04 13:34:08 2024 +0000 |
| b |
| @@ -1,51 +1,51 @@ -mz r k s classes centers tstatistics p.values adj.p.values -328.916687011719 1 3 2 2 99.8858636414327 1.70552696059604 0.18663997985398 1 -287.833343505859 1 3 2 2 7.93884077274423 0.892316549633065 0.437965610367674 1 -255.41667175293 1 3 2 2 26.7994657596825 0.631134212003395 0.572759961955499 1 -345.166687011719 1 3 2 1 21.0950943140054 0.576828686839774 0.59496246236433 1 -345.75 1 3 2 1 0.000773752341530878 0.482319170719424 0.654784520667766 1 -329 1 3 2 2 74.8624360093532 0.475284801312334 0.667045276242305 1 -304.583343505859 1 3 2 1 5.04842009181125 0.450156816961743 0.675916423005788 1 -220.083343505859 1 3 2 2 10.2419118378809 0.420529464581692 0.702404905639997 1 -344.5 1 3 2 2 8.15512536650391 0.363646985142304 0.740237670889389 1 -344.583343505859 1 3 2 2 5.4215950014828 0.304403127899382 0.780714952248732 1 -345.25 1 3 2 1 5.27367451972173 0.268889305324497 0.801314134156555 1 -227.083343505859 1 3 2 1 10.6095966735402 0.131855388448792 0.901465021716936 1 -241.16667175293 1 3 2 2 10.2228356643606 0.00899373598928799 0.993388776797424 1 -200.083343505859 1 3 2 1 5.29581279081497 0 1 1 -200.16667175293 1 3 2 1 2.49731024427445 0 1 1 -200.25 1 3 2 1 4.24962276503692 0 1 1 -200.333343505859 1 3 2 1 4.16908612899782 0 1 1 -200.41667175293 1 3 2 1 0.989885497306688 0 1 1 -200.5 1 3 2 1 0.0378717820621928 0 1 1 -200.583343505859 1 3 2 1 2.81878248323476e-05 0 1 1 -200.66667175293 1 3 2 1 1.26528769673667e-06 0 1 1 -200.75 1 3 2 1 0.666464703081512 0 1 1 -200.833343505859 1 3 2 1 3.6413484204556 0 1 1 -200.91667175293 1 3 2 1 3.45873609261615 0 1 1 -201 1 3 2 1 1.58100572954213 0 1 1 -201.083343505859 1 3 2 1 0.2813029079667 0 1 1 -201.16667175293 1 3 2 1 4.42209759159998e-14 0 1 1 -201.25 1 3 2 1 3.41779163861997e-17 0 1 1 -201.333343505859 1 3 2 1 0.000253170100352953 0 1 1 -201.41667175293 1 3 2 1 0.00016447017446336 0 1 1 -201.5 1 3 2 1 0.000183867881986821 0 1 1 -201.583343505859 1 3 2 1 4.80801683375459e-05 0 1 1 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31.4346115567144 5383218.86513272 +334.916687011719 2 3 2 3 30.2348653251492 5177760.72539743 +356.916687011719 2 3 2 3 25.8992680025733 4435283.91063335 +268.75 2 3 2 3 24.8843994788257 4261486.32454463 +337.083343505859 2 3 2 3 24.076154950511 4123072.93009932 +223.083343505859 2 3 2 3 23.5238106008253 4028483.66742955 +322.75 2 3 2 3 21.1392607565015 3620126.33132717 +336.833343505859 2 3 2 3 20.6620308683609 3538400.07750469 +355.166687011719 2 3 2 3 18.4907168150306 3166559.65455431 +320.916687011719 2 3 2 3 17.2063877644047 2946616.59442457 +353.083343505859 2 3 2 3 16.8234420417854 2881036.62949622 +336.75 2 3 2 3 16.7187790997581 2863112.96130508 +243.083343505859 2 3 2 3 15.5592704357313 2660685.15930393 +239 2 3 2 3 14.2720642237061 2430842.6371766 +353 2 3 2 3 13.5307668741903 2317161.62252572 +322.833343505859 2 3 2 3 12.8046812967398 2192818.50053318 +335 2 3 2 3 12.3652778492893 2117570.0750485 +253.16667175293 2 3 2 3 12.0854610616434 2069651.07756065 +357 2 3 2 3 11.9569353060518 2038504.20368564 +239.083343505859 2 3 2 3 11.0827784286314 1894560.07739424 +304.416687011719 2 3 2 3 10.887666846709 1864526.67041401 +355.083343505859 2 3 2 3 10.683244498926 1829519.62400645 +253.083343505859 2 3 2 3 9.45150829766949 1618583.15936374 +337.166687011719 2 3 2 3 9.33301677641879 1598291.31087568 +271.916687011719 2 3 2 3 9.12359299784904 1562427.22761811 +320.833343505859 2 3 2 3 8.73450243650785 1495794.9508762 +337 2 3 2 3 8.5146049237488 1458136.74587279 +223.16667175293 2 3 2 3 7.98093294393921 1362811.60628815 +356.833343505859 2 3 2 3 7.09002484849993 1214175.97414669 +321 2 3 2 3 5.39634988238388 924131.880905024 +336.916687011719 2 3 2 3 4.48411788419812 767910.936489358 +353.166687011719 2 3 2 3 4.27552914584328 732189.837289735 +322.666687011719 2 3 2 3 2.96529598280259 507810.663415085 +253.25 2 3 2 3 2.57840437701005 441554.960739003 +201.083343505859 2 3 2 3 2.53171579058899 433559.381070877 +239.16667175293 2 3 2 3 2.2953225607321 393008.209560118 +322.916687011719 2 3 2 3 2.28058136169889 390552.224077165 +357.083343505859 2 3 2 3 1.70686479002556 291914.8539171 +335.083343505859 2 3 2 3 1.4768205245555 252907.259131211 +304.916687011719 2 3 2 3 1.24070335904165 212471.880129018 +337.25 2 3 2 3 1.14493988502698 196072.257688371 +268.666656494141 2 3 2 3 0.92667513041734 158694.127820549 +223.25 2 3 2 3 0.82702373927433 141133.073322158 +334.833343505859 2 3 2 3 6.29302594522327 140030.740579744 +336.666687011719 2 3 2 3 0.635433257415288 108818.209778545 +352.916687011719 2 3 2 3 0.623417256360104 106760.813070652 +271.833343505859 2 3 2 3 21.1169003038898 106529.616944863 +232.75 2 3 2 3 17.5453756989052 88550.3222933331 |