# 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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+