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changeset 13:40395e60d2be draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
author rv43
date Fri, 08 Apr 2022 17:49:28 +0000
parents 27d4a36a8c4a
children 50c8d19d5f89
files config_l_center.yaml run_tomo_find_center run_tomo_reconstruct run_tomo_setup tomo.py tomo_find_center.py tomo_find_center.xml
diffstat 7 files changed, 24 insertions(+), 94 deletions(-) [+]
line wrap: on
line diff
--- a/config_l_center.yaml	Fri Apr 08 16:56:53 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-bright_field:
-  data_path: /nfs/chess/scratch/user/rv43/2022-1/id3b/sobhani-3249-A/tomo7C/tomo7C_flat_ANDOR2_001.h5
-  img_offset: 1
-  img_start: 0
-  num: 20
-dark_field:
-  data_path: null
-  img_start: -1
-  num: 0
-data_filetype: h5
-detector:
-  columns: 1700
-  id: andor2
-  pixel_size: 0.0013
-  rows: 1436
-preprocess:
-  img_x_bounds:
-  - 0
-  - 1436
-  num_theta_skip: 0
-  zoom_perc: 100
-stack_info:
-  num: 1
-  stacks:
-  - data_path: /nfs/chess/scratch/user/rv43/2022-1/id3b/sobhani-3249-A/tomo7C/tomo7C_ANDOR2_001.h5
-    img_offset: 1
-    img_start: 0
-    index: 1
-    num: 354
-    preprocessed: true
-    ref_height: 0.0
-theta_range:
-  end: 180.0
-  num: 354
-  start: 0.0
-work_folder: /nfs/chess/scratch/user/rv43/2022-1/id3b/sobhani-3249-A
--- a/run_tomo_find_center	Fri Apr 08 16:56:53 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#!/bin/bash
-
-#python tomo_find_center.py -i red_stacks.npz -c 'config_l_center.yaml' --row_bounds 620 950 --center_rows 670 890 --output_config 'output.yaml' --recon_center_low 'recon_center_low.png' --recon_center_upp 'recon_center_upp.png'
-python tomo_find_center.py -i red_stacks.npz -c 'config_l_center.yaml' --row_bounds 620 950 --center_rows 670 890 --output_config 'output.yaml' --recon_center_low 'recon_center_low.png' --recon_center_upp 'recon_center_upp.png' --center_type_selector 'vo' --set_range 2 --set_step 0.9
-#python tomo_find_center.py -i red_stacks.npz -c 'config_l_center.yaml' --row_bounds 620 950 --center_rows 670 890 --output_config 'output.yaml' --recon_center_low 'recon_center_low.png' --recon_center_upp 'recon_center_upp.png' --center_type_selector 'user' --set_center 10 --set_range 2 --set_step 0.9
--- a/run_tomo_reconstruct	Fri Apr 08 16:56:53 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-python tomo_reconstruct.py -i red_stacks.npz -c 'config_l_recon.yaml' --output_config 'output.yaml' --output_data 'output.npz'
--- a/run_tomo_setup	Fri Apr 08 16:56:53 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-python tomo_setup.py -i inputfiles_l.txt -c 'config_l_setup.yaml' --theta_range '0.0 180.0 354' --output_config 'output.yaml' --output_data 'output.npz' --dark 'dark.png' --bright 'bright.png' --tomo 'tomo.png' --detectorbounds 'detectorbounds.png' 1 20 1 354
--- a/tomo.py	Fri Apr 08 16:56:53 2022 +0000
+++ b/tomo.py	Fri Apr 08 17:49:28 2022 +0000
@@ -1149,14 +1149,14 @@
         logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!')
         return recon_clean
 
-    def _plotEdgesOnePlane(self, recon_plane, title, path=None, name=None, weight=0.001):
+    def _plotEdgesOnePlane(self, recon_plane, title, path=None, weight=0.001):
         # RV parameters for the denoise, gaussian, and ring removal will be different for different feature sizes
         edges = denoise_tv_chambolle(recon_plane, weight = weight)
         vmax = np.max(edges[0,:,:])
         vmin = -vmax
         if self.galaxy_flag:
-            msnc.quickImshow(edges[0,:,:], title, path=path, name=name, save_fig=True,
-                    save_only=True, cmap='gray', vmin=vmin, vmax=vmax)
+            msnc.quickImshow(edges[0,:,:], title, path=path, save_fig=True, save_only=True,
+                    cmap='gray', vmin=vmin, vmax=vmax)
         else:
             if path is None:
                 path=self.output_folder
@@ -1168,9 +1168,13 @@
         del edges
 
     def _findCenterOnePlane(self, sinogram, row, thetas_deg, eff_pixel_size, cross_sectional_dim,
-            tol=0.1, num_core=1, recon_pngname=None, galaxy_param=None):
+            tol=0.1, num_core=1, galaxy_param=None):
         """Find center for a single tomography plane.
         """
+        if self.galaxy_flag:
+            assert(galaxy_param)
+            if not os.path.exists('find_center_pngs'):
+                os.mkdir('find_center_pngs')
         # sinogram index order: theta,column
         # need index order column,theta for iradon, so take transpose
         sinogram_T = sinogram.T
@@ -1185,23 +1189,19 @@
             return float(center_offset_vo)
         elif self.galaxy_flag:
             logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
-            if recon_pngname:
-                assert(isinstance(recon_pngname, str))
-                recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
-                        eff_pixel_size, cross_sectional_dim, False, num_core)
-                title = os.path.basename(recon_pngname)
-                self._plotEdgesOnePlane(recon_plane, title, name=recon_pngname)
-                del recon_plane
-            if not galaxy_param or not galaxy_param['center_type_selector']:
+            recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
+                    eff_pixel_size, cross_sectional_dim, False, num_core)
+            title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
+            self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
+            del recon_plane
+            if not galaxy_param['center_type_selector']:
                 del sinogram_T
                 return float(center_offset_vo)
         else:
             print(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}')
-            if recon_pngname:
-                logging.warning('Ignoring recon_pngname in _findCenterOnePlane (only for Galaxy)')
             recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
                     eff_pixel_size, cross_sectional_dim, False, num_core)
-            title = f'edges row{row} center_offset_vo{center_offset_vo:.2f}'
+            title = f'edges row{row} center offset{center_offset_vo:.2f} Vo'
             self._plotEdgesOnePlane(recon_plane, title)
         if not self.galaxy_flag:
             if (pyip.inputYesNo('Try finding center using phase correlation '+
@@ -1218,7 +1218,7 @@
                 print(f'Center at row {row} using phase correlation = {center_offset:.2f}')
                 recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg,
                         eff_pixel_size, cross_sectional_dim, False, num_core)
-                title = f'edges row{row} center_offset{center_offset:.2f}'
+                title = f'edges row{row} center_offset{center_offset:.2f} PC'
                 self._plotEdgesOnePlane(recon_plane, title)
             if (pyip.inputYesNo('Accept a center location ([y]) or continue '+
                     'search (n)? ', blank=True) != 'no'):
@@ -1232,8 +1232,6 @@
                 return float(center_offset)
 
         # perform center finding search
-        if self.galaxy_flag and not os.path.exists('png_files'):
-            os.mkdir('png_files')
         while True:
             if self.galaxy_flag and galaxy_param and galaxy_param['center_type_selector']:
                 set_center = center_offset_vo
@@ -1271,7 +1269,7 @@
                         thetas_deg, eff_pixel_size, cross_sectional_dim, False, num_core)
                 title = f'edges row{row} center_offset{center_offset:.2f}'
                 if self.galaxy_flag:
-                    self._plotEdgesOnePlane(recon_plane, title, path='png_files')
+                    self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs')
                 else:
                     self._plotEdgesOnePlane(recon_plane, title)
             if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ',
@@ -1760,13 +1758,9 @@
                 if self.save_plots_only:
                     msnc.clearFig(f'theta={theta_start}')
             # center_stack order: row,theta,column
-            if galaxy_param:
-                recon_pngname = galaxy_param['recon_center_low']
-            else:
-                recon_pngname = None
             center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
                     eff_pixel_size, cross_sectional_dim, num_core=num_core,
-                    recon_pngname=recon_pngname, galaxy_param=galaxy_param)
+                    galaxy_param=galaxy_param)
         logging.info(f'lower_center_offset = {center_offset:.2f} {type(center_offset)}')
         print(center_offset)
 
@@ -1809,13 +1803,9 @@
                 if self.save_plots_only:
                     msnc.clearFig(f'theta={theta_start}')
             # center_stack order: row,theta,column
-            if galaxy_param:
-                recon_pngname = galaxy_param['recon_center_upp']
-            else:
-                recon_pngname = None
             center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg,
                     eff_pixel_size, cross_sectional_dim, num_core=num_core,
-                    recon_pngname=recon_pngname, galaxy_param=galaxy_param)
+                    galaxy_param=galaxy_param)
         logging.info(f'upper_center_offset = {center_offset:.2f}')
         del center_stack
 
--- a/tomo_find_center.py	Fri Apr 08 16:56:53 2022 +0000
+++ b/tomo_find_center.py	Fri Apr 08 17:49:28 2022 +0000
@@ -30,10 +30,6 @@
             type=float, help='Set step')
     parser.add_argument('--output_config',
             required=True, help='Output config')
-    parser.add_argument('--recon_center_low',
-            help='Lower reconstructed slice center image name')
-    parser.add_argument('--recon_center_upp',
-            help='Upper reconstructed slice center image name')
     parser.add_argument('-l', '--log', 
             type=argparse.FileType('w'), default=sys.stdout, help='Log file')
     args = parser.parse_args()
@@ -56,8 +52,6 @@
     logging.debug(f'set_range = {args.set_range}')
     logging.debug(f'set_step = {args.set_step}')
     logging.debug(f'output_config = {args.output_config}')
-    logging.debug(f'recon_center_low = {args.recon_center_low}')
-    logging.debug(f'recon_center_upp = {args.recon_center_upp}')
     logging.debug(f'log = {args.log}')
     logging.debug(f'is log stdout? {args.log is sys.stdout}')
 
@@ -74,8 +68,7 @@
     # Find centers
     galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows,
             'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center, 
-            'set_range' : args.set_range, 'set_step' : args.set_step, 
-            'recon_center_low' : args.recon_center_low, 'recon_center_upp' : args.recon_center_upp}
+            'set_range' : args.set_range, 'set_step' : args.set_step}
     tomo.findCenters(galaxy_param)
 
 if __name__ == "__main__":
--- a/tomo_find_center.xml	Fri Apr 08 16:56:53 2022 +0000
+++ b/tomo_find_center.xml	Fri Apr 08 17:49:28 2022 +0000
@@ -5,9 +5,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        #if str( $set.set_selector ) == "yes"
-            mkdir png_files;
-        #end if
+        mkdir find_center_pngs;
         $__tool_directory__/tomo_find_center.py
         -i '$red_stacks'
         -c '$config'
@@ -22,8 +20,6 @@
             --set_step '$set.set_step'
         #end if
         --output_config 'output_config.yaml'
-        --recon_center_low 'recon_center_low.png'
-        --recon_center_upp 'recon_center_upp.png'
         -l '$log'
     ]]></command>
     <inputs>
@@ -59,14 +55,12 @@
     </inputs>
     <outputs>
         <expand macro="common_outputs"/>
-        <data name="recon_center_low" format="png" label="Recontructed slice lower center using Nghia Vo’s method" from_work_dir="recon_center_low.png"/>
-        <data name="recon_center_upp" format="png" label="Recontructed slice upper center using Nghia Vo’s method" from_work_dir="recon_center_upp.png"/>
-        <collection name="recon_center_set" type="list" label="Recontructed slices center position set">
-            <discover_datasets pattern="__name_and_ext__" directory="png_files"/>
+        <collection name="recon_center_set" type="list" label="Recontructed slices at various centers">
+            <discover_datasets pattern="__name_and_ext__" directory="find_center_pngs"/>
         </collection>
     </outputs>
     <help><![CDATA[
-        Preprocess tomography images.
+        Find the center axis for a tomography reconstruction.
     ]]></help>
     <expand macro="citations"/>
 </tool>