Mercurial > repos > rv43 > tomo
changeset 31:063e1e847d95 draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit bd7bbc4facb864b77e56b8c22bcbb497d1815e95"
| author | rv43 |
|---|---|
| date | Mon, 18 Apr 2022 21:54:56 +0000 |
| parents | c4a90d5b1ed2 |
| children | b1f92b63f84c |
| files | tomo.py |
| diffstat | 1 files changed, 10 insertions(+), 6 deletions(-) [+] |
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--- a/tomo.py Mon Apr 18 21:40:06 2022 +0000 +++ b/tomo.py Mon Apr 18 21:54:56 2022 +0000 @@ -1183,7 +1183,6 @@ center = sinogram.shape[1]/2 # try automatic center finding routines for initial value - #num_core=1 tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) center_offset_vo = tomo_center-center if self.test_mode: @@ -1301,6 +1300,7 @@ # RV should we remove rings? # https://tomopy.readthedocs.io/en/latest/api/tomopy.misc.corr.html # RV: Add an option to do (extra) secondary iterations later or to do some sort of convergence test? + print(f'OK AA row_bounds = {row_bounds}') if row_bounds is None: row_bounds = [0, tomo_stack.shape[0]] else: @@ -1318,15 +1318,18 @@ raise ValueError('center_offsets dimension mismatch in reconstructOneTomoStack') centers = center_offsets centers += tomo_stack.shape[2]/2 + print(f'num_core = {num_core}') + print(f'thetas = {thetas}') + print(f'centers = {centers}') if True: tomo_stack = tomopy.prep.stripe.remove_stripe_fw( tomo_stack[row_bounds[0]:row_bounds[1]], sigma=sigma, ncore=num_core) else: tomo_stack = tomo_stack[row_bounds[0]:row_bounds[1]] - print('OK AA') + print('OK BB') tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, sinogram_order=True, algorithm=algorithm, ncore=num_core) - print('OK BB') + print('OK CC') if run_secondary_sirt and secondary_iter > 0: #options = {'method':'SIRT_CUDA', 'proj_type':'cuda', 'num_iter':secondary_iter} #RV: doesn't work for me: "Error: CUDA error 803: system has unsupported display driver / @@ -1339,7 +1342,7 @@ tomo_recon_stack = tomopy.recon(tomo_stack, thetas, centers, init_recon=tomo_recon_stack, options=options, sinogram_order=True, algorithm=tomopy.astra, ncore=num_core) - print('OK CC') + print('OK DD') if True: tomopy.misc.corr.remove_ring(tomo_recon_stack, rwidth=rwidth, out=tomo_recon_stack, ncore=num_core) @@ -1456,6 +1459,7 @@ """ if num_core is None: num_core = self.num_core + logging.info(f'num_core = {self.num_core}') # Try loading any already preprocessed stacks (skip in Galaxy) # preprocessed stack order for each one in stack: row,theta,column stack_info = self.config['stack_info'] @@ -1539,6 +1543,7 @@ """ if num_core is None: num_core = self.num_core + logging.info(f'num_core = {self.num_core}') logging.debug('Find centers for tomography stacks') stacks = self.config['stack_info']['stacks'] available_stacks = [stack['index'] for stack in stacks if stack.get('preprocessed', False)] @@ -1890,6 +1895,7 @@ """ if num_core is None: num_core = self.num_core + logging.info(f'num_core = {self.num_core}') if self.galaxy_flag: assert(galaxy_param) if not os.path.exists('center_slice_pngs'): @@ -1990,13 +1996,11 @@ 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() - num_core = 1 print(f'OK4 {i} c') self.tomo_recon_stacks[i]= self._reconstructOneTomoStack(self.tomo_stacks[i], thetas, center_offsets=center_offsets, sigma=0.1, num_core=num_core, algorithm='gridrec', run_secondary_sirt=True, secondary_iter=25) print(f'OK4 {i} d') - exit('Done') logging.info(f'Reconstruction of stack {index} took {time()-t0:.2f} seconds!') if self.galaxy_flag: x_slice = int(self.tomo_stacks[i].shape[0]/2)