changeset 93:c63315c31cef draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit b682c580a95bebc59bc33128973cee4eac8362c7
author ximgchess
date Wed, 24 May 2023 14:33:59 +0000
parents 142f73036013
children 5479b4b4f0e6
files saxswaxs/PIL5.poni saxswaxs/PIL5.tif saxswaxs/pipeline.yaml saxswaxs/test_1d saxswaxs/test_1d_001/test_1d_PIL11_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_010.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_010.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_010.tiff tomo/pipeline_combine.yaml tomo/pipeline_find_center.yaml tomo/pipeline_reconstruct.yaml tomo/pipeline_reduce_nexus.yaml tomo/pipeline_reduce_yaml.yaml tomo/test.txt tomo/tmp.txt tomo/tomo_combine.xml tomo/tomo_macros.xml tomo/tomo_reduce.xml
diffstat 47 files changed, 138 insertions(+), 101 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/PIL5.poni	Wed May 24 14:33:59 2023 +0000
@@ -0,0 +1,12 @@
+# Nota: C-Order, 1 refers to the Y axis, 2 to the X axis 
+# Calibration done at Wed Dec  1 09:43:02 2021
+poni_version: 2
+Detector: Pilatus300k
+Detector_config: {}
+Distance: 1.6482087488134558
+Poni1: 0.1678687786895594
+Poni2: 0.13236163515363114
+Rot1: 0.05582857735072926
+Rot2: -0.07300334677284326
+Rot3: 3.757385675073369e-05
+Wavelength: 1.2781876020248165e-10
Binary file saxswaxs/PIL5.tif has changed
--- a/saxswaxs/pipeline.yaml	Wed May 24 13:55:45 2023 +0000
+++ b/saxswaxs/pipeline.yaml	Wed May 24 14:33:59 2023 +0000
@@ -1,14 +1,5 @@
 pipeline:
 
-  # Download example data
-  - common.URLReader:
-      url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/saxswaxs%2frawdata_test_1d.tar/raw?ref=main
-      headers:
-        PRIVATE-TOKEN: # your token here
-  - common.URLResponseProcessor
-  - common.ExtractArchiveWriter:
-      filename: .
-
   # Collect map data
   - common.YAMLReader:
       filename: map.yaml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/test_1d	Wed May 24 14:33:59 2023 +0000
@@ -0,0 +1,92 @@
+#F sample_14_align
+#E 1637195555
+#D Wed Nov 17 19:32:35 2021
+#C spec  User = chess_id3b
+
+#O0 mono  monz  mchi  mony  monx  und_CL  s0s  s0n
+#O1 s0t  s0b  s0x  s0h  s0z  s0v  mirzu  mirzd
+#O2 mirbu  mirbd  xu  yu  zu  xd  zld  zrd
+#O3 fpx  att  mirz  mirth  s3b  s3t  s3s  s3n
+#O4 s3z  s3v  s3x  s3h  s1b  s1t  s1s  s1n
+#O5 s1z  s1v  s1x  s1h  fl1x  fl1z  fl2x  fl2z
+#O6 waxx  waxz1  waxz2  waxz  waxtilt  xmirx  xmirz  xmirphi
+#O7 xmirth  saxx  saxy  saxz  andy  andz  zl2  xl2
+#O8 yl2  yr2  zru2  zrd2  xd7  zd7  xu7  zu7
+#O9 bedx_lo  icvx  icvz  air_x  p3y  p3z  nozx  nozz
+#O10 bedx  bedx_galil  s2b  s2t  s2s  s2n  s2z  s2v
+#O11 s2x  s2h  xrfx  xrfy  xrfz  zd5  zru5  zlu5
+#O12 yd5  xd5  xu5  tabx5  zr6  zlu6  zld6  yr6
+#O13 yl6  xr6  th  tth  phi  vtxx  txr  tyr
+#O14 tzr  txt  tyt  tzt  txr2  tyr2  tzr2  txt2
+#O15 tyt2  tzt2  txr3  tyr3  tzr3  txt3  tyt3  tzt3
+#O16 txr4  tyr4  tzr4  txt4  tyt4  tzt4  txr5  tyr5
+#O17 tzr5  txt5  tyt5  tzt5  txr6  tyr6  tzr6  txt6
+#O18 tyt6  tzt6  txr7  tyr7  tzr7  txt7  tyt7  tzt7
+#O19 txr8  tyr8  tzr8  txt8  tyt8  tzt8  
+#o0 mono monz mchi mony monx und s0s s0n
+#o1 s0t s0b s0x s0h s0z s0v mirzu mirzd
+#o2 mirbu mirbd xu yu zu xd zld zrd
+#o3 fpx att mirz mirth s3b s3t s3s s3n
+#o4 s3z s3v s3x s3h s1b s1t s1s s1n
+#o5 s1z s1v s1x s1h fl1x fl1z fl2x fl2z
+#o6 waxx waxz1 waxz2 waxz waxtilt xmirx xmirz xmirphi
+#o7 xmirth saxx saxy saxz andy andz zl2 xl2
+#o8 yl2 yr2 zru2 zrd2 xd7 zd7 xu7 zu7
+#o9 bedx_lo icvx icvz air_x p3y p3z nozx nozz
+#o10 bedx bedx_g s2b s2t s2s s2n s2z s2v
+#o11 s2x s2h samx samy samz zd5 zru5 zlu5
+#o12 yd5 xd5 xu5 tabx5 zr6 zlu6 zld6 yr6
+#o13 yl6 xr6 th tth phi vtxx txr tyr
+#o14 tzr txt tyt tzt txr2 tyr2 tzr2 txt2
+#o15 tyt2 tzt2 txr3 tyr3 tzr3 txt3 tyt3 tabz
+#o16 txr4 tyr4 tzr4 txt4 tyt4 tzt4 txr5 tyr5
+#o17 tzr5 txt5 tyt5 tzt5 txr6 tyr6 tzr6 txt6
+#o18 tyt6 tzt6 txr7 tyr7 tzr7 crlx tyt7 crlz
+#o19 txr8 tyr8 tzr8 txt8 bedy bedz 
+#J0 Seconds  ic0_ni  keyz  icv_pos  icv_sum  tminus  sec_2  diode
+#J1 ic1  ic3  icv_lo  icv_hi  mot_pulse  p11_r1  
+#j0 sec ic0_ni keyz icv_pos icv_sum tminus sec_2 diode
+#j1 ic1 ic3 icv_lo icv_hi pulses p11_r1 
+
+
+#S 1  flyscan samx 140.9 141.5 10 0.1 
+#D Wed Nov 17 19:35:47 2021
+#T 12  (Seconds)
+#G0 0
+#G1 0
+#G3 0
+#G4 0
+#Q 
+#P0 -3.7830971 3.0011801 -0.22821594 -3.8 13.94 3.69 34.924802 35.874722
+#P1 20.129699 18.629511 35.399834 0.94995949 19.379555 1.5001232 9.3153197 6.2847224
+#P2 7.6113723e-07 -3.039743e-07 3.4829819 1.005207 -9.6873251 -4.7275845 -10.608966 -10.438151
+#P3 -10.972008 544.544 7.8 -3.4595 -0.004199987 0.34579999 1.76 2.1600002
+#P4 0.1708 0.35 1.96 0.4 -1.35 -0.85000006 -0.30000002 0.40000036
+#P5 -1.1 0.5 0.05 0.7 -1.5328934 -20.102657 -8.9922526 -3.4989075
+#P6 11.303603 27.619064 29.211176 28.415 0.796 -3.0517576e-08 0.058524542 3.516674e-09
+#P7 0.49999989 8 1 -6 170 5.1999999 -11.341377 -4.0548513
+#P8 0.91678883 0.91679319 -9.7110746 -7.5862294 1.1553852 -0.19508918 4.0468633 -0.2839906
+#P9 11.900876 0.13366788 2.9005861 -1.2465739 385.49999 70 -13.999995 9.9999998
+#P10 -4.3098231e-06 -174.51549 -1.2799991 -0.37999994 2.8299999 3.5300016 -0.83 0.9
+#P11 3.18 0.7 140.8975 26.999999 141.6 1.0000013 4.0000013 4.0000013
+#P12 6.8038999 -0.59999922 -0.59999922 292 -20.93269 -45.083693 -11.619761 4.6857093e-09
+#P13 1.5745194e-08 -8.0676912 8.5449218e-08 90 0 9.1661255e-07 -1.1665 0.3365
+#P14 11.4515 -0.4805 1.496 -10.1055 4.183 3.7555 0 -2.5
+#P15 -0.815 -9.995 -0.0065 -0.081 -9 14.9515 0.0045 -0.4
+#P16 9.228 -1.1635 -9.65 0.4 -4.3845 1.0185 -2.201 0
+#P17 0 -0.6 8.1215 2.5 55.4955 5.769 0 -4.1045
+#P18 -38.1255 -24.9045 0.234 0.234 7.609 1.2315 0.234 -0.1975
+#P19 -10.2505 -10.2505 -0.6675 -10.2505 0 0 
+#N 9
+#L xrfx  Seconds  sec_2  diode  ic1  ic3  icv_lo  icv_hi  mot_pulse  
+140.899995 0 0.302713 10898.0 14772.0 29927.0 93811.0 87169.0 0
+140.959995 0 0.100783 3615.0 4910.0 9950.0 30648.0 29072.0 0
+141.019995 0 0.099614 3592.0 4902.0 9951.0 30359.0 28781.0 0
+141.079995 0 0.099614 1264.0 4851.0 9819.0 30288.0 28727.0 0
+141.139995 0 0.099614 877.0 4709.0 9445.0 30411.0 28511.0 0
+141.199995 0 0.100398 631.0 4764.0 9537.0 30308.0 28751.0 0
+141.259995 0 0.100782 542.0 4804.0 9630.0 30359.0 28916.0 0
+141.319995 0 0.099614 625.0 4839.0 9743.0 30425.0 28762.0 0
+141.379995 0 0.099614 542.0 4787.0 9597.0 30298.0 28635.0 0
+141.439995 0 0.099614 665.0 4784.0 9599.0 30283.0 28662.0 0
+141.499995 0 0.146491 1248.0 6957.0 13906.0 44347.0 42023.0 0
Binary file saxswaxs/test_1d_001/test_1d_PIL11_001_000.tiff has changed
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Binary file saxswaxs/test_1d_001/test_1d_PIL9_001_009.tiff has changed
Binary file saxswaxs/test_1d_001/test_1d_PIL9_001_010.tiff has changed
--- a/tomo/pipeline_combine.yaml	Wed May 24 13:55:45 2023 +0000
+++ b/tomo/pipeline_combine.yaml	Wed May 24 14:33:59 2023 +0000
@@ -1,11 +1,11 @@
 pipeline:
 
   # Combine tomography stacks
-  - pipeline.MultiplePipelineItem:
-      items:
-        - common.NexusReader:
+  - common.MultipleReader:
+      readers:
+        - NexusReader:
             filename: reconstructed.nex
-        - common.YAMLReader:
+        - YAMLReader:
             filename: combine.yaml
             schema: TomoCombineConfig
   - tomo.TomoDataProcessor:
--- a/tomo/pipeline_find_center.yaml	Wed May 24 13:55:45 2023 +0000
+++ b/tomo/pipeline_find_center.yaml	Wed May 24 14:33:59 2023 +0000
@@ -1,11 +1,11 @@
 pipeline:
 
   # Find rotation axis centers for the tomography stacks
-  - pipeline.MultiplePipelineItem:
-      items:
-        - common.NexusReader:
+  - common.MultipleReader:
+      readers:
+        - NexusReader:
             filename: reduced.nex
-        - common.YAMLReader:
+        - YAMLReader:
             filename: find_center.yaml
             schema: TomoFindCenterConfig
   - tomo.TomoDataProcessor:
--- a/tomo/pipeline_reconstruct.yaml	Wed May 24 13:55:45 2023 +0000
+++ b/tomo/pipeline_reconstruct.yaml	Wed May 24 14:33:59 2023 +0000
@@ -1,14 +1,14 @@
 pipeline:
 
   # Reconstruct tomography stacks
-  - pipeline.MultiplePipelineItem:
-      items:
-        - common.NexusReader:
+  - common.MultipleReader:
+      readers:
+        - NexusReader:
             filename: reduced.nex
-        - common.YAMLReader:
+        - YAMLReader:
             filename: reconstruct.yaml
             schema: TomoReconstructConfig
-        - common.YAMLReader:
+        - YAMLReader:
             filename: centers.yaml
             schema: TomoFindCenterConfig
   - tomo.TomoDataProcessor:
--- a/tomo/pipeline_reduce_nexus.yaml	Wed May 24 13:55:45 2023 +0000
+++ b/tomo/pipeline_reduce_nexus.yaml	Wed May 24 14:33:59 2023 +0000
@@ -1,11 +1,11 @@
 pipeline:
 
   # Reduce tomography images
-  - pipeline.MultiplePipelineItem:
-      items:
-        - common.NexusReader:
+  - common.MultipleReader:
+      readers:
+        - NexusReader:
             filename: setup.nex
-        - common.YAMLReader:
+        - YAMLReader:
             filename: reduce.yaml
             schema: TomoReduceConfig
   - tomo.TomoDataProcessor:
--- a/tomo/pipeline_reduce_yaml.yaml	Wed May 24 13:55:45 2023 +0000
+++ b/tomo/pipeline_reduce_yaml.yaml	Wed May 24 14:33:59 2023 +0000
@@ -1,12 +1,12 @@
 pipeline:
 
   # Reduce tomography images
-  - pipeline.MultiplePipelineItem:
-      items:
-        - common.YAMLReader:
+  - common.MultipleReader:
+      readers:
+        - YAMLReader:
             filename: map.yaml
             schema: MapConfig
-        - common.YAMLReader:
+        - YAMLReader:
             filename: reduce.yaml
             schema: TomoReduceConfig
   - tomo.TomoDataProcessor:
--- a/tomo/test.txt	Wed May 24 13:55:45 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-I had a Galaxy tool crash repeatedly on Friday and tried a bunch of things, but nothing helped. Today I tried it from scratch and kept notes:
-
-Removed everything in:
- /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess
-and in:
-/nfs/chess/galaxy-dev/var/dependencies/_conda/envs
-
-Rebooted the ansible
-
-Made sure that the repo in the testtoolshed is up to date.
-
-Reinstall the CHAP tool at:
-https://galaxy-dev.classe.cornell.edu/admin/toolshed
-Watching its progress, I can see that it first clones the tool repo and then installs the tool dependencies.
-When done, I have the following new content in the galaxy tree:
-ls -al /nfs/chess/galaxy-dev/var/dependencies/_conda/envs:
-drwxr-xr-x 3 galaxy galaxy 32 May  1 09:17 .
-drwxr-xr-x 5 galaxy galaxy 52 Apr 28 08:40 ..
-drwxr-xr-x 3 galaxy galaxy 26 May  1 09:18 chap_test_20230411
-
-ls -al /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess:
-drwxr-xr-x  6 galaxy galaxy  317 May  1 10:04 .
-drwxr-xr-x 15 galaxy galaxy  226 Aug 29  2021 ..
-drwxr-xr-x 12 galaxy galaxy  184 May  1 10:03 __ChessAnalysisPipeline@0.0.2
--rw-r--r--  1 galaxy galaxy    0 May  1 09:18 .conda_envs_dir_test
-drwxr-xr-x 27 galaxy galaxy 4096 May  1 10:02 mulled-v1-0cd3a5ccc731743d38833d0396752d8219d106c20bb3bb478c34e74608ecb1c3
-drwxr-xr-x 26 galaxy galaxy 4096 May  1 09:51 mulled-v1-67ac3841866ce74ad34393f2abb6cc61f6651a9d3f3e677b9821c88c9b0a676e
-drwxr-xr-x 12 galaxy galaxy  184 May  1 10:04 mulled-v1-b1085bc9e4a5d280004f5b197e8295b3ef5167ea9ea22a074defb863f1b86458
-
-When running a Galaxy tool and only when I try to pip install certif-pyspec, it bombs with:
-OSError: [Errno 30] Read-only file system: '__config__.cpython-310.pyc'
-
-See stdout and stderr in:
-/nfs/chess/aux/reduced_data/user/galaxy-dev/jobs/002/2440/outputs
--- a/tomo/tmp.txt	Wed May 24 13:55:45 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-try:
-    from pyspec.file.spec import FileSpec
-    from pyspec.file.tiff import TiffFile
-except:
-    import sys
-    home = '/home/galaxy'
-    localpippath = f'{home}/.local/lib/python3.11/site-packages'
-    if localpippath not in sys.path:
-        sys.path.insert(0, localpippath)
-    from pyspec.file.spec import FileSpec
-    from pyspec.file.tiff import TiffFile
-
-
--- a/tomo/tomo_combine.xml	Wed May 24 13:55:45 2023 +0000
+++ b/tomo/tomo_combine.xml	Wed May 24 14:33:59 2023 +0000
@@ -7,7 +7,7 @@
     <command detect_errors="exit_code">
         <![CDATA[
         mkdir tomo_combine_plots;
-        cp $input_file reconstructed.nex &&
+        cp $input_file reconstruced.nex &&
         cp $tool_config combine.yaml &&
         CHAP --config 
         $__tool_directory__/pipeline_combine.yaml
--- a/tomo/tomo_macros.xml	Wed May 24 13:55:45 2023 +0000
+++ b/tomo/tomo_macros.xml	Wed May 24 14:33:59 2023 +0000
@@ -1,10 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">0.1.0</token>
     <token name="@PROFILE@">21.09</token>
-    <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>
+    <token name="@PYTHON_TEMPLATE_VERSION@">3.9</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.0.8">chessanalysispipeline</requirement>
+            <requirement type="package" version="0.0.7">chessanalysispipeline</requirement>
             <requirement type="package" version="1.1.0">lmfit</requirement>
             <requirement type="package" version="3.7.1">matplotlib</requirement>
             <requirement type="package" version="1.0.1">nexusformat</requirement>
@@ -15,17 +15,13 @@
     <xml name="citations">
         <citations>
             <citation type="bibtex">
-@software{keara_soloway_2023_7963605,
-  author       = {Keara Soloway and
-                  Valentin Kuznetsov and
-                  Rolf Verberg},
-  title        = {CHESSComputing/ChessAnalysisPipeline: v0.0.8},
-  month        = may,
-  year         = 2023,
-  publisher    = {Zenodo},
-  version      = {v0.0.8},
-  doi          = {10.5281/zenodo.7963605},
-  url          = {https://doi.org/10.5281/zenodo.7963605}
+@misc{githubChessAnalysisPipeline,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {Tomography reconstruction},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
 }</citation>
         </citations>
     </xml>
--- a/tomo/tomo_reduce.xml	Wed May 24 13:55:45 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed May 24 14:33:59 2023 +0000
@@ -8,12 +8,9 @@
         <![CDATA[
         mkdir tomo_reduce_plots;
         #if str($map.type_selector) == "yaml"
+            $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
             cp $input_file map.yaml &&
-            #if str($map.detector.type_selector) == "from_file"
-                cat $map.detector.detector_file $tool_config > reduce.yaml &&
-            #else
-                cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml &&
-            #end if
+            cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml &&
         #else
             cp $input_file setup.nex &&
             cp $tool_config reduce.yaml &&
@@ -49,18 +46,14 @@
             <when value="yaml">
                 <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/>
                 <conditional name="detector">
-                    <param name="type_selector" type="select" display="radio" label="Choose detector">
+                    <param name="type_selector" type="select" display="radio" label="Choose detector prefix">
                         <option value="andor2.yaml">andor2</option>
                         <option value="manta.yaml">manta</option>
                         <option value="retiga.yaml">retiga</option>
-                        <option value="from_file">from file</option>
                     </param>
                     <when value="andor2.yaml"/>
                     <when value="manta.yaml"/>
                     <when value="retiga.yaml"/>
-                    <when value="from_file">
-                        <param name="detector_file" type="data" format="yaml" optional="false" label="Detector config file"/>
-                    </when>
                 </conditional>
             </when>
             <when value="nexus">