Mercurial > repos > rv43 > tomo
diff tomo.py @ 28:c7211931fc99 draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 99f399daf512578b317aca74314e0246faa65cec"
| author | rv43 |
|---|---|
| date | Mon, 18 Apr 2022 21:26:01 +0000 |
| parents | 9d631a5e118f |
| children | 59c5c0b53579 |
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--- a/tomo.py Mon Apr 18 21:18:05 2022 +0000 +++ b/tomo.py Mon Apr 18 21:26:01 2022 +0000 @@ -1183,8 +1183,7 @@ center = sinogram.shape[1]/2 # try automatic center finding routines for initial value - num_core=1 - #tomo_center = tomopy.find_center_vo(sinogram, ncore=1) + #num_core=1 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) center_offset_vo = tomo_center-center if self.test_mode: @@ -1973,7 +1972,7 @@ assert(stack.get('preprocessed', False) == True) assert(stack.get('reconstructed', False) == True) continue - print(f'OK4 {i} b') + print(f'OK4 {i} b size = {self.tomo_stacks[i].size}') stack['reconstructed'] = False if not self.tomo_stacks[i].size: self.tomo_stacks[i], available = self._loadTomo('red stack', index, @@ -1983,7 +1982,9 @@ stack[i]['preprocessed'] = False load_error = True continue + print(f'lower_row = {lower_row} upper_row = {upper_row} self.tomo_stacks[i].shape[0] = {self.tomo_stacks[i].shape[0]}') assert(0 <= lower_row < upper_row < self.tomo_stacks[i].shape[0]) + print(f'OK4 {i} c') center_offsets = [lower_center_offset-lower_row*center_slope, upper_center_offset+(self.tomo_stacks[i].shape[0]-1-upper_row)*center_slope] t0 = time() @@ -1991,7 +1992,7 @@ 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!') - print(f'OK4 {i} c') + print(f'OK4 {i} d') if self.galaxy_flag: x_slice = int(self.tomo_stacks[i].shape[0]/2) title = f'{basetitle} {index} xslice{x_slice}' @@ -2025,7 +2026,7 @@ if combine_stacks and index in combine_stacks.get('stacks', []): combine_stacks['stacks'].remove(index) self.cf.saveFile(self.config_out) - print(f'OK4 {i} d') + print(f'OK4 {i} e') # Save reconstructed tomography stack to file print('OK5')