# HG changeset patch
# User rv43
# Date 1679338908 0
# Node ID 05335876d167bc3dcd2a8dc91fb5179f3fcc6af4
# Parent  543dba81eb1595c5ccf9f041c45ea9f133632183
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty

diff -r 543dba81eb15 -r 05335876d167 __pycache__/fit.cpython-39.pyc
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diff -r 543dba81eb15 -r 05335876d167 __pycache__/general.cpython-39.pyc
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diff -r 543dba81eb15 -r 05335876d167 run_tomo_reduce
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_tomo_reduce	Mon Mar 20 19:01:48 2023 +0000
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# From workflow
+#python -m workflow run_tomo -i sobhani-3249-A.yaml -o sobhani-3249-A_reduce.nxs -n 48 -s 'only' --reduce_data
+#python -m workflow run_tomo -i tenstom_1304r-1_one_stack.yaml -o tenstom_1304r-1_one_stack_reduce.nxs -n 48 -s 'only' --reduce_data
+#python -m workflow run_tomo -i tenstom_1304r-1.yaml -o tenstom_1304r-1_reduce.nxs -n 48 -s 'only' --reduce_data
+
+# As Galaxy tool:
+python tomo_reduce.py -i "../../../Tomo/sobhani-3249-A_start.nxs" -o sobhani-3249-A_reduce.nxs --log_level INFO -l tomo.log --galaxy_flag --img_x_bounds -1 -1
+#python tomo_reduce.py -i tenstom_1304r-1_one_stack_start.nxs -o tenstom_1304r-1_one_stack_reduce.nxs --log_level INFO -l tomo.log --galaxy_flag #--img_x_bounds 582 1509
+#python tomo_reduce.py -i tenstom_1304r-1_start.nxs -o tenstom_1304r-1_reduce.nxs --log_level INFO -l tomo.log --galaxy_flag #--img_x_bounds 713 1388
diff -r 543dba81eb15 -r 05335876d167 tomo.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo.log	Mon Mar 20 19:01:48 2023 +0000
@@ -0,0 +1,4 @@
+2023-03-20 15:01:16,794 : INFO - tomo_reduce : __main__ - input_file = ../../../Tomo/sobhani-3249-A_start.nxs
+2023-03-20 15:01:16,794 : INFO - tomo_reduce : __main__ - output_file = sobhani-3249-A_reduce.nxs
+2023-03-20 15:01:16,794 : INFO - tomo_reduce : __main__ - galaxy_flag = True
+2023-03-20 15:01:16,794 : INFO - tomo_reduce : __main__ - img_x_bounds = [-1, -1]
diff -r 543dba81eb15 -r 05335876d167 tomo_reduce.py
--- a/tomo_reduce.py	Mon Mar 20 18:54:48 2023 +0000
+++ b/tomo_reduce.py	Mon Mar 20 19:01:48 2023 +0000
@@ -79,7 +79,7 @@
 
     # Read input file
     data = tomo.read(args.input_file)
-    print('data:\n{data.tree}')
+    print(f'data:\n{data.tree}')
     return
 
     # Generate reduced tomography images
diff -r 543dba81eb15 -r 05335876d167 tomo_reduce.xml
--- a/tomo_reduce.xml	Mon Mar 20 18:54:48 2023 +0000
+++ b/tomo_reduce.xml	Mon Mar 20 19:01:48 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.2" python_template_version="3.9">
+<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.3" python_template_version="3.9">
     <description>Reduce tomography images</description>
     <macros>
         <import>tomo_macros.xml</import>
diff -r 543dba81eb15 -r 05335876d167 workflow/.run_tomo.py.swp
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diff -r 543dba81eb15 -r 05335876d167 workflow/__pycache__/__version__.cpython-39.pyc
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diff -r 543dba81eb15 -r 05335876d167 workflow/__pycache__/models.cpython-39.pyc
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diff -r 543dba81eb15 -r 05335876d167 workflow/__pycache__/run_tomo.cpython-39.pyc
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diff -r 543dba81eb15 -r 05335876d167 workflow/run_tomo.py
--- a/workflow/run_tomo.py	Mon Mar 20 18:54:48 2023 +0000
+++ b/workflow/run_tomo.py	Mon Mar 20 19:01:48 2023 +0000
@@ -874,11 +874,10 @@
         # Select image bounds
         title = f'tomography image at theta={round(theta, 2)+0}'
         if img_x_bounds is not None:
-            if is_int_pair(img_x_bounds)i and img_x_bounds[0] == -1 and img_x_bounds[1] == -1
+            if is_int_pair(img_x_bounds) and img_x_bounds[0] == -1 and img_x_bounds[1] == -1:
                 img_x_bounds = None
-            elif not is_index_range(img_x_bounds, ge=0,
-                le=first_image.shape[0])):
-            raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})')
+            elif not is_index_range(img_x_bounds, ge=0, le=first_image.shape[0]):
+                raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})')
         if nxentry.instrument.source.attrs['station'] in ('id1a3', 'id3a'):
             pixel_size = nxentry.instrument.detector.x_pixel_size
             # Try to get a fit from the bright field