Mercurial > repos > rv43 > tomo
changeset 21:3caba2116858 draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit e32e37ee46f47b185f924884685eb1d464761e86"
| author | rv43 |
|---|---|
| date | Mon, 18 Apr 2022 19:43:15 +0000 |
| parents | c033f8843dc0 |
| children | ac2f726f9054 |
| files | tomo.py tomo_reconstruct.py tomo_reconstruct.xml |
| diffstat | 3 files changed, 28 insertions(+), 20 deletions(-) [+] |
line wrap: on
line diff
--- a/tomo.py Mon Apr 18 18:10:07 2022 +0000 +++ b/tomo.py Mon Apr 18 19:43:15 2022 +0000 @@ -1883,15 +1883,17 @@ def reconstructTomoStacks(self, galaxy_param=None, num_core=None): """Reconstruct tomography stacks. """ - print('OK1') if num_core is None: num_core = self.num_core + if self.galaxy_flag: + assert(galaxy_param) + if not os.path.exists('center_slice_pngs'): + os.mkdir('center_slice_pngs') logging.debug('Reconstruct tomography stacks') stacks = self.config['stack_info']['stacks'] assert(len(self.tomo_stacks) == self.config['stack_info']['num']) assert(len(self.tomo_stacks) == len(stacks)) assert(len(self.tomo_recon_stacks) == len(stacks)) - print('OK2') if self.galaxy_flag: assert(isinstance(galaxy_param, dict)) # Get rotation axis centers @@ -1907,7 +1909,6 @@ galaxy_param = None lower_center_offset = None upper_center_offset = None - print('OK3') # Get rotation axis rows and centers find_center = self.config['find_center'] @@ -1934,7 +1935,6 @@ center_slope = (upper_center_offset-lower_center_offset)/(upper_row-lower_row) # Set thetas (in radians) - print('OK4') theta_range = self.config['theta_range'] theta_start = theta_range['start'] theta_end = theta_range['end'] @@ -1943,11 +1943,10 @@ thetas = np.radians(np.linspace(theta_start, theta_end, int(num_theta/(num_theta_skip+1)), endpoint=False)) - print('OK5') # Reconstruct tomo stacks zoom_perc = self.config['preprocess'].get('zoom_perc', 100) if zoom_perc == 100: - basetitle = 'recon stack full' + basetitle = 'recon stack fullres' else: basetitle = f'recon stack {zoom_perc}p' load_error = False @@ -1971,7 +1970,6 @@ if not self.tomo_stacks[i].size: self.tomo_stacks[i], available = self._loadTomo('red stack', index, required=True) - print(f'self.tomo_stacks.shape = {self.tomo_stacks[i].shape}') if not self.tomo_stacks[i].size: logging.error(f'Unable to load tomography stack {index} for reconstruction') stack[i]['preprocessed'] = False @@ -1985,23 +1983,32 @@ thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core, algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25) logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!') - if not self.test_mode and not self.galaxy_flag: - row_slice = int(self.tomo_stacks[i].shape[0]/2) - title = f'{basetitle} {index} slice{row_slice}' - msnc.quickImshow(self.tomo_recon_stacks[i][row_slice,:,:], title=title, + if self.galaxy_flag: + x_slice = int(self.tomo_stacks[i].shape[0]/2) + title = f'{basetitle} {index} xslice{x_slice}' + msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title, + path='center_slice_pngs', save_fig=True, save_only=True) + y_slice = int(self.tomo_stacks[i].shape[0]/2) + title = f'{basetitle} {index} yslice{y_slice}' + msnc.quickImshow(self.tomo_recon_stacks[i][:,y_slice,:], title=title, + path='center_slice_pngs', save_fig=True, save_only=True) + z_slice = int(self.tomo_stacks[i].shape[0]/2) + title = f'{basetitle} {index} zslice{z_slice}' + msnc.quickImshow(self.tomo_recon_stacks[i][:,:,z_slice], title=title, + path='center_slice_pngs', save_fig=True, save_only=True) + elif not self.test_mode: + x_slice = int(self.tomo_stacks[i].shape[0]/2) + title = f'{basetitle} {index} xslice{x_slice}' + msnc.quickImshow(self.tomo_recon_stacks[i][x_slice,:,:], title=title, path=self.output_folder, save_fig=self.save_plots, save_only=self.save_plots_only) msnc.quickPlot(self.tomo_recon_stacks[i] - [row_slice,int(self.tomo_recon_stacks[i].shape[2]/2),:], + [x_slice,int(self.tomo_recon_stacks[i].shape[2]/2),:], title=f'{title} cut{int(self.tomo_recon_stacks[i].shape[2]/2)}', path=self.output_folder, save_fig=self.save_plots, save_only=self.save_plots_only) self._saveTomo('recon stack', self.tomo_recon_stacks[i], index) -# else: -# np.savetxt(self.output_folder+f'recon_stack_{index}.txt', -# self.tomo_recon_stacks[i][row_slice,:,:], fmt='%.6e') self.tomo_stacks[i] = np.array([]) - print('OK6') # Update config and save to file stack['reconstructed'] = True @@ -2010,7 +2017,6 @@ combine_stacks['stacks'].remove(index) self.cf.saveFile(self.config_out) - print('OK7') # Save reconstructed tomography stack to file if self.galaxy_flag: t0 = time()
--- a/tomo_reconstruct.py Mon Apr 18 18:10:07 2022 +0000 +++ b/tomo_reconstruct.py Mon Apr 18 19:43:15 2022 +0000 @@ -61,10 +61,8 @@ # Reconstruct tomography stacks galaxy_param = {'center_offsets' : args.center_offsets, 'output_name' : args.output_data} - print(f'Here galaxy_param = {galaxy_param}') logging.info(f'galaxy_param = {galaxy_param}') tomo.reconstructTomoStacks(galaxy_param) - print('Here') # Displaying memory usage logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
--- a/tomo_reconstruct.xml Mon Apr 18 18:10:07 2022 +0000 +++ b/tomo_reconstruct.xml Mon Apr 18 19:43:15 2022 +0000 @@ -5,11 +5,12 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ + mkdir center_slice_pngs; $__tool_directory__/tomo_reconstruct.py -i '$red_stacks' -c '$config' --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset - --output_data 'output.npz' + --output_data 'output_data.npz' --output_config 'output_config.yaml' -l '$log' ]]></command> @@ -24,6 +25,9 @@ <outputs> <expand macro="common_outputs"/> <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/> + <collection name="recon_slices" type="list" label="Recontructed slices midway in each dimension"> + <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/> + </collection> </outputs> <help><![CDATA[ Reconstruct tomography images.