Mercurial > repos > rv43 > tomo
changeset 22:ac2f726f9054 draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit c38e9cb882bb790d6a5994b836719d1df494c92b"
| author | rv43 |
|---|---|
| date | Mon, 18 Apr 2022 19:55:01 +0000 |
| parents | 3caba2116858 |
| children | 3e336f5b6402 |
| files | tomo.py |
| diffstat | 1 files changed, 7 insertions(+), 2 deletions(-) [+] |
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--- a/tomo.py Mon Apr 18 19:43:15 2022 +0000 +++ b/tomo.py Mon Apr 18 19:55:01 2022 +0000 @@ -1183,6 +1183,7 @@ center = sinogram.shape[1]/2 # try automatic center finding routines for initial value + print('OK2') tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) center_offset_vo = tomo_center-center if self.test_mode: @@ -1196,6 +1197,7 @@ title = f'edges row{row} center offset{center_offset_vo:.2f} Vo' self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs') del recon_plane + print(f'center_type_selector = {center_type_selector}') if not galaxy_param['center_type_selector']: del sinogram_T return float(center_offset_vo) @@ -1263,6 +1265,7 @@ min=1, max=center_offset_upp-center_offset_low) num_center_offset = 1+int((center_offset_upp-center_offset_low)/center_offset_step) center_offsets = np.linspace(center_offset_low, center_offset_upp, num_center_offset) + print(f'center_offsets = {center_offsets}') for center_offset in center_offsets: if center_offset == center_offset_vo: continue @@ -1274,6 +1277,7 @@ self._plotEdgesOnePlane(recon_plane, title, path='find_center_pngs') else: self._plotEdgesOnePlane(recon_plane, title) + print('OK3') if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ', min=0, max=1): break @@ -1719,7 +1723,6 @@ use_center = 'no' row = center_rows[0] if self.test_mode or self.galaxy_flag: - logging.info(f'row = {row} n1 = {n1} n2 = {n2}') assert(msnc.is_int(row, n1, n2-2)) if msnc.is_int(row, n1, n2-2): if self.test_mode or self.galaxy_flag: @@ -1782,6 +1785,8 @@ if msnc.is_num(center_offset): use_center = pyip.inputYesNo('Current upper center offset = '+ f'{center_offset}, use this value ([y]/n)? ', blank=True) + logging.info(f'use_center = {use_center}') + logging.info(f'use_row = {use_row}') if use_center == 'no': if use_row == 'no': if not self.test_mode: @@ -1794,7 +1799,7 @@ if self.save_plots_only: msnc.clearFig(f'theta={theta_start}') # center_stack order: row,theta,column - center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg, + center_offset = self._findOenterOnePlane(center_stack[row,:,:], row, thetas_deg, eff_pixel_size, cross_sectional_dim, num_core=num_core, galaxy_param=galaxy_param) logging.info(f'upper_center_offset = {center_offset:.2f}')