# HG changeset patch
# User rv43
# Date 1679420436 0
# Node ID 0891477bcb16e61eb3f11b2b68b2786e17ed1c9c
# Parent  fbbd829383036f17e8896e1f5ab5359f9df14d93
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty

diff -r fbbd82938303 -r 0891477bcb16 run_tomo_reduce
--- a/run_tomo_reduce	Tue Mar 21 16:47:44 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#!/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 fbbd82938303 -r 0891477bcb16 tomo_find_center.xml
--- a/tomo_find_center.xml	Tue Mar 21 16:47:44 2023 +0000
+++ b/tomo_find_center.xml	Tue Mar 21 17:40:36 2023 +0000
@@ -17,7 +17,7 @@
     </command>
     <inputs>
         <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
-        <section name="center_rows" title="Reconstruction row bounds">
+        <section name="center_rows" title="Find center axis planes">
             <param name="low" type="integer" value="-1" label="Lower bound"/>
             <param name="upp" type="integer" value="-1" label="Upper bound"/>
         </section>
diff -r fbbd82938303 -r 0891477bcb16 tomo_reconstruct.xml
--- a/tomo_reconstruct.xml	Tue Mar 21 16:47:44 2023 +0000
+++ b/tomo_reconstruct.xml	Tue Mar 21 17:40:36 2023 +0000
@@ -12,12 +12,22 @@
             --center_file "$center_file"
             --output_file "output.nex"
             --galaxy_flag
+            --x_bounds $x_bounds.low $x_bounds.upp
+            --y_bounds $y_bounds.low $y_bounds.upp
             -l "$log"
         ]]>
     </command>
     <inputs>
         <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
         <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
+        <section name="x_bounds" title="Boundaries of reconstructed images in x-direction">
+            <param name="low" type="integer" value="-1" label="Lower bound"/>
+            <param name="upp" type="integer" value="-1" label="Upper bound"/>
+        </section>
+        <section name="y_bounds" title="Boundaries of reconstructed images in y-direction">
+            <param name="low" type="integer" value="-1" label="Lower bound"/>
+            <param name="upp" type="integer" value="-1" label="Upper bound"/>
+        </section>
     </inputs>
     <outputs>
         <expand macro="common_outputs"/>
diff -r fbbd82938303 -r 0891477bcb16 tomo_reduce.xml
--- a/tomo_reduce.xml	Tue Mar 21 16:47:44 2023 +0000
+++ b/tomo_reduce.xml	Tue Mar 21 17:40:36 2023 +0000
@@ -11,16 +11,25 @@
             --input_file "$input_file"
             --output_file "output.nex"
             --galaxy_flag
-            --img_x_bounds $img_x_bounds.low $img_x_bounds.upp
+            #if str($img_bounds.type_selector) == "enter_range"
+                --img_x_bounds $img_bounds.low $img_bounds.upp
+            #end if
             -l "$log"
         ]]>
     </command>
     <inputs>
         <param name="input_file" type="data" optional="false" label="Input file"/>
-        <section name="img_x_bounds" title="Reduction x bounds">
-            <param name="low" type="integer" value="-1" label="Lower bound"/>
-            <param name="upp" type="integer" value="-1" label="Upper bound"/>
-        </section>
+        <conditional name="img_bounds">
+            <param name="type_selector" type="select" label="Choose image range for data reduction">
+                <option value="full_range" selected="true">Use the full image range</option>
+                <option value="enter_range">Manually enter the image range</option>
+            </param>
+            <when value="full_range"/>
+            <when value="enter_range">
+                <param name="low" type="integer" optional="false" label="Lower image range index in vertical direction"/>
+                <param name="upp" type="integer" optional="false" label="Upper image range index in vertical direction"/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <expand macro="common_outputs"/>
diff -r fbbd82938303 -r 0891477bcb16 workflow/run_tomo.py
--- a/workflow/run_tomo.py	Tue Mar 21 16:47:44 2023 +0000
+++ b/workflow/run_tomo.py	Tue Mar 21 17:40:36 2023 +0000
@@ -517,10 +517,10 @@
             y_bounds = self.test_config.get('y_bounds')
             z_bounds = None
         elif self.galaxy_flag:
-            if x_bounds is not None and not is_int_pair(x_bounds, ge=0,
+            if x_bounds is not None and not is_int_pair(x_bounds, ge=-1,
                     lt=tomo_recon_stacks[0].shape[1]):
                 raise ValueError(f'Invalid parameter x_bounds ({x_bounds})')
-            if y_bounds is not None and not is_int_pair(y_bounds, ge=0,
+            if y_bounds is not None and not is_int_pair(y_bounds, ge=-1,
                     lt=tomo_recon_stacks[0].shape[1]):
                 raise ValueError(f'Invalid parameter y_bounds ({y_bounds})')
             z_bounds = None
@@ -887,11 +887,6 @@
 
         # 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) 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})')
         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
@@ -993,6 +988,8 @@
             if self.galaxy_flag:
                 if img_x_bounds is None:
                     img_x_bounds = (0, first_image.shape[0])
+                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})')
             else:
                 quick_imshow(first_image, title=title)
                 print('Select vertical data reduction range from first tomography image')