# HG changeset patch
# User rv43
# Date 1649435947 0
# Node ID ec7c3e84d6116ce965328f7af07afc85960155f2
# Parent e3c8a96d2f67f6b018fe77774d353e25cb523eeb
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6d01e142af3a0daad7ab37d4ff02d0f1797057a7"
diff -r e3c8a96d2f67 -r ec7c3e84d611 __pycache__/msnc_tools.cpython-39.pyc
Binary file __pycache__/msnc_tools.cpython-39.pyc has changed
diff -r e3c8a96d2f67 -r ec7c3e84d611 __pycache__/tomo.cpython-39.pyc
Binary file __pycache__/tomo.cpython-39.pyc has changed
diff -r e3c8a96d2f67 -r ec7c3e84d611 config_l_center.yaml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/config_l_center.yaml Fri Apr 08 16:39:07 2022 +0000
@@ -0,0 +1,36 @@
+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
diff -r e3c8a96d2f67 -r ec7c3e84d611 run_tomo_find_center
--- a/run_tomo_find_center Fri Apr 08 15:06:16 2022 +0000
+++ b/run_tomo_find_center Fri Apr 08 16:39:07 2022 +0000
@@ -1,3 +1,5 @@
#!/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'
+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
diff -r e3c8a96d2f67 -r ec7c3e84d611 tomo.py
--- a/tomo.py Fri Apr 08 15:06:16 2022 +0000
+++ b/tomo.py Fri Apr 08 16:39:07 2022 +0000
@@ -1149,18 +1149,20 @@
logging.debug(f'filtering and removing ring artifact took {time()-t0:.2f} seconds!')
return recon_clean
- def _plotEdgesOnePlane(self, recon_plane, title, name=None, weight=0.001):
+ def _plotEdgesOnePlane(self, recon_plane, title, path=None, name=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, name=name, save_fig=True, save_only=True,
- cmap='gray', vmin=vmin, vmax=vmax)
+ msnc.quickImshow(edges[0,:,:], title, path=path, name=name, save_fig=True,
+ save_only=True, cmap='gray', vmin=vmin, vmax=vmax)
else:
- msnc.quickImshow(edges[0,:,:], f'{title} coolwarm', path=self.output_folder,
+ if path is None:
+ path=self.output_folder
+ msnc.quickImshow(edges[0,:,:], f'{title} coolwarm', path=path,
save_fig=self.save_plots, save_only=self.save_plots_only, cmap='coolwarm')
- msnc.quickImshow(edges[0,:,:], f'{title} gray', path=self.output_folder,
+ msnc.quickImshow(edges[0,:,:], f'{title} gray', path=path,
save_fig=self.save_plots, save_only=self.save_plots_only, cmap='gray',
vmin=vmin, vmax=vmax)
del edges
@@ -1230,6 +1232,8 @@
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
@@ -1266,7 +1270,10 @@
recon_plane = self._reconstructOnePlane(sinogram_T, center_offset+center,
thetas_deg, eff_pixel_size, cross_sectional_dim, False, num_core)
title = f'edges row{row} center_offset{center_offset:.2f}'
- self._plotEdgesOnePlane(recon_plane, title)
+ if self.galaxy_flag:
+ self._plotEdgesOnePlane(recon_plane, title, path='png_files')
+ else:
+ self._plotEdgesOnePlane(recon_plane, title)
if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ',
min=0, max=1):
break
diff -r e3c8a96d2f67 -r ec7c3e84d611 tomo_find_center.xml
--- a/tomo_find_center.xml Fri Apr 08 15:06:16 2022 +0000
+++ b/tomo_find_center.xml Fri Apr 08 16:39:07 2022 +0000
@@ -5,6 +5,9 @@
-
+