# HG changeset patch # User ximgchess # Date 1681228193 0 # Node ID 84a215623d9e6fbfaea9f3f6b9869a86735656ce # Parent 47d2a1f087d12e43f17e4e3b79ceb57cd6dabce1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a diff -r 47d2a1f087d1 -r 84a215623d9e saxswaxs/ignoreshed.yml --- a/saxswaxs/ignoreshed.yml Tue Apr 11 14:41:16 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -name: chap_test_20230328 -owner: kls286 -description: A generic test pipeline for CHAP -remote_repository_url: https://github.com/CHESSComputing/ChessAnalysisPipeline -type: unrestricted -categories: -- Structural Materials Analysis diff -r 47d2a1f087d1 -r 84a215623d9e saxswaxs/klspipeline.yaml --- a/saxswaxs/klspipeline.yaml Tue Apr 11 14:41:16 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -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: glpat-sH-sniHbynCxUDJBpv5V # your token here - - common.URLResponseProcessor - - common.ExtractArchiveWriter: - filename: . - - # Collect map data - - common.YAMLReader: - filename: map.yaml - schema: MapConfig - - common.MapProcessor - - common.NexusWriter: - filename: map_specdata.nxs - force_overwrite: true - - # Integrate map detetcor data - - common.MultipleReader: - readers: - - YAMLReader: - filename: map.yaml - schema: MapConfig - - YAMLReader: - filename: integration.yaml - schema: IntegrationConfig - - common.IntegrateMapProcessor - - common.NexusWriter: - filename: map_reduceddata.nxs - force_overwrite: true diff -r 47d2a1f087d1 -r 84a215623d9e tomo/andor2.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/andor2.yaml Tue Apr 11 15:49:53 2023 +0000 @@ -0,0 +1,8 @@ +detector: + prefix: andor2 + rows: 1436 + columns: 1700 + pixel_size: + - 0.0065 + - 0.0065 + lens_magnification: 5.0 diff -r 47d2a1f087d1 -r 84a215623d9e tomo/pipeline_reduce_nexus.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/pipeline_reduce_nexus.yaml Tue Apr 11 15:49:53 2023 +0000 @@ -0,0 +1,14 @@ +pipeline: + + # Reduce tomography images + - common.MultipleReader: + readers: + - NexusReader: + filename: setup.nex + - YAMLReader: + filename: reduce.yaml + schema: TomoReduceConfig + - tomo.TomoDataProcessor + - common.NexusWriter: + filename: output.nex + force_overwrite: true diff -r 47d2a1f087d1 -r 84a215623d9e tomo/pipeline_reduce_yaml.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/pipeline_reduce_yaml.yaml Tue Apr 11 15:49:53 2023 +0000 @@ -0,0 +1,15 @@ +pipeline: + + # Reduce tomography images + - common.MultipleReader: + readers: + - YAMLReader: + filename: map.yaml + schema: MapConfig + - YAMLReader: + filename: reduce.yaml + schema: TomoReduceConfig + - tomo.TomoDataProcessor + - common.NexusWriter: + filename: output.nex + force_overwrite: true diff -r 47d2a1f087d1 -r 84a215623d9e tomo/tomo_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/tomo_macros.xml Tue Apr 11 15:49:53 2023 +0000 @@ -0,0 +1,29 @@ + + 0.1.0 + 21.09 + 3.9.13 + + + chessanalysispipeline + lmfit + matplotlib + nexusformat + pydantic + tomopy + + + + + +@misc{githubChessAnalysisPipeline, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {Tomography reconstruction}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/CHESSComputing/ChessAnalysisPipeline}, +} + + + + diff -r 47d2a1f087d1 -r 84a215623d9e tomo/tomo_reduce.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/tomo_reduce.xml Tue Apr 11 15:49:53 2023 +0000 @@ -0,0 +1,102 @@ + + Reduce tomography images + + tomo_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +