Mercurial > repos > rv43 > tomo
changeset 7:845270a96464 draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
| author | rv43 |
|---|---|
| date | Thu, 07 Apr 2022 21:09:58 +0000 |
| parents | baf9f5eef128 |
| children | 9cabd6e746d3 |
| files | msnc_tools.py tomo.py tomo_find_center.py tomo_find_center.xml tomo_macros.xml tomo_reconstruct.xml tomo_setup.xml |
| diffstat | 7 files changed, 238 insertions(+), 154 deletions(-) [+] |
line wrap: on
line diff
--- a/msnc_tools.py Wed Apr 06 19:48:22 2022 +0000 +++ b/msnc_tools.py Thu Apr 07 21:09:58 2022 +0000 @@ -619,9 +619,8 @@ if not os.path.isfile(config_file): logging.error(f'Unable to load {config_file}') return - print(f'\nLoading {config_file}\n') - # Load config file + # Load config file (for now for Galaxy, allow .dat extension) self.suffix = os.path.splitext(config_file)[1] if self.suffix == '.yml' or self.suffix == '.yaml' or self.suffix == '.dat': with open(config_file, 'r') as f:
--- a/tomo.py Wed Apr 06 19:48:22 2022 +0000 +++ b/tomo.py Thu Apr 07 21:09:58 2022 +0000 @@ -1166,7 +1166,7 @@ del edges def _findCenterOnePlane(self, sinogram, row, thetas_deg, eff_pixel_size, cross_sectional_dim, - tol=0.1, num_core=1, recon_pngname=None): + tol=0.1, num_core=1, recon_pngname=None, galaxy_param=None): """Find center for a single tomography plane. """ # sinogram index order: theta,column @@ -1177,79 +1177,106 @@ # try automatic center finding routines for initial value tomo_center = tomopy.find_center_vo(sinogram, ncore=num_core) center_offset_vo = tomo_center-center - if self.test_mode or self.galaxy_flag: + if self.test_mode: + logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') + del sinogram_T + return float(center_offset_vo) + elif self.galaxy_flag: logging.info(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') - if self.test_mode: + if recon_pngname: + assert(isinstance(recon_pngname, str)) + recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg, + eff_pixel_size, cross_sectional_dim, False, num_core) + title = os.path.basename(recon_pngname) + self._plotEdgesOnePlane(recon_plane, title, name=recon_pngname) + del recon_plane + if not galaxy_param or not galaxy_param['center_type_selector']: del sinogram_T return float(center_offset_vo) else: print(f'Center at row {row} using Nghia Vo’s method = {center_offset_vo:.2f}') if recon_pngname: logging.warning('Ignoring recon_pngname in _findCenterOnePlane (only for Galaxy)') - recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg, - eff_pixel_size, cross_sectional_dim, False, num_core) - if self.galaxy_flag: - assert(isinstance(recon_pngname, str)) - title = os.path.basename(recon_pngname) - self._plotEdgesOnePlane(recon_plane, title, name=recon_pngname) - del sinogram_T - del recon_plane - return float(center_offset_vo) - else: - title = f'edges row{row} center_offset_vo{center_offset_vo:.2f}' - self._plotEdgesOnePlane(recon_plane, title) - if (pyip.inputYesNo('Try finding center using phase correlation '+ - '(y/[n])? ', blank=True) == 'yes'): - tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1, - rotc_guess=tomo_center) - error = 1. - while error > tol: - prev = tomo_center - tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol, - rotc_guess=tomo_center) - error = np.abs(tomo_center-prev) - center_offset = tomo_center-center - print(f'Center at row {row} using phase correlation = {center_offset:.2f}') recon_plane = self._reconstructOnePlane(sinogram_T, tomo_center, thetas_deg, eff_pixel_size, cross_sectional_dim, False, num_core) - title = f'edges row{row} center_offset{center_offset:.2f}' + title = f'edges row{row} center_offset_vo{center_offset_vo:.2f}' self._plotEdgesOnePlane(recon_plane, title) - if (pyip.inputYesNo('Accept a center location ([y]) or continue '+ - 'search (n)? ', blank=True) != 'no'): - del sinogram_T - del recon_plane - center_offset = pyip.inputNum( - f' Enter chosen center offset [{-int(center)}, {int(center)}] '+ - f'([{center_offset_vo}])): ', blank=True) - if center_offset == '': - center_offset = center_offset_vo - return float(center_offset) + if not self.galaxy_flag: + if (pyip.inputYesNo('Try finding center using phase correlation '+ + '(y/[n])? ', blank=True) == 'yes'): + tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=0.1, + rotc_guess=tomo_center) + error = 1. + while error > tol: + prev = tomo_center + tomo_center = tomopy.find_center_pc(sinogram, sinogram, tol=tol, + rotc_guess=tomo_center) + error = np.abs(tomo_center-prev) + center_offset = tomo_center-center + print(f'Center at row {row} using phase correlation = {center_offset:.2f}') + recon_plane = self._reconstructOnePlane(sinogram_T, tomo_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 (pyip.inputYesNo('Accept a center location ([y]) or continue '+ + 'search (n)? ', blank=True) != 'no'): + center_offset = pyip.inputNum( + f' Enter chosen center offset [{-int(center)}, {int(center)}] '+ + f'([{center_offset_vo:.2f}])): ', blank=True) + if center_offset == '': + center_offset = center_offset_vo + del sinogram_T + del recon_plane + return float(center_offset) + # perform center finding search while True: - center_offset_low = pyip.inputInt('\nEnter lower bound for center offset '+ - f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center)) - center_offset_upp = pyip.inputInt('Enter upper bound for center offset '+ - f'[{center_offset_low}, {int(center)}]: ', - min=center_offset_low, max=int(center)) - if center_offset_upp == center_offset_low: - center_offset_step = 1 + if self.galaxy_flag and galaxy_param and galaxy_param['center_type_selector']: + set_center = center_offset_vo + if galaxy_param['center_type_selector'] == 'user': + set_center = galaxy_param['set_center'] + set_range = galaxy_param['set_range'] + center_offset_step = galaxy_param['set_step'] + if (not msnc.is_num(set_range, 0) or not msnc.is_num(center_offset_step) or + center_offset_step <= 0): + logging.warning('Illegal center finding search parameter, skip search') + del sinogram_T + return float(center_offset_vo) + set_range = center_offset_step*max(1, int(set_range/center_offset_step)) + center_offset_low = set_center-set_range + center_offset_upp = set_center+set_range else: - center_offset_step = pyip.inputInt('Enter step size for center offset search '+ - f'[1, {center_offset_upp-center_offset_low}]: ', - min=1, max=center_offset_upp-center_offset_low) - for center_offset in range(center_offset_low, center_offset_upp+center_offset_step, - center_offset_step): - logging.info(f'center_offset = {center_offset}') + center_offset_low = pyip.inputInt('\nEnter lower bound for center offset '+ + f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center)) + center_offset_upp = pyip.inputInt('Enter upper bound for center offset '+ + f'[{center_offset_low}, {int(center)}]: ', + min=center_offset_low, max=int(center)) + if center_offset_upp == center_offset_low: + center_offset_step = 1 + else: + center_offset_step = pyip.inputInt('Enter step size for center offset search '+ + f'[1, {center_offset_upp-center_offset_low}]: ', + 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) + for center_offset in center_offsets: + if center_offset == center_offset_vo: + continue + logging.info(f'center_offset = {center_offset:.2f}') 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}' + title = f'edges row{row} center_offset{center_offset:.2f}' self._plotEdgesOnePlane(recon_plane, title) - if pyip.inputInt('\nContinue (0) or end the search (1): ', min=0, max=1): + if self.galaxy_flag or pyip.inputInt('\nContinue (0) or end the search (1): ', + min=0, max=1): break del sinogram_T del recon_plane - center_offset = pyip.inputNum(f' Enter chosen center offset '+ + if self.galaxy_flag: + center_offset = center_offset_vo + else: + center_offset = pyip.inputNum(f' Enter chosen center offset '+ f'[{-int(center)}, {int(center)}]: ', min=-int(center), max=int(center)) return float(center_offset) @@ -1513,8 +1540,7 @@ stack['ref_height'] = stack['ref_height']+pixel_size self.cf.saveFile(self.config_out) - def findCenters(self, row_bounds=None, center_rows=None, recon_low_pngname=None, - recon_upp_pngname=None, num_core=None): + def findCenters(self, galaxy_param=None, num_core=None): """Find rotation axis centers for the tomography stacks. """ if num_core is None: @@ -1524,23 +1550,26 @@ available_stacks = [stack['index'] for stack in stacks if stack.get('preprocessed', False)] logging.debug('Available stacks: {available_stacks}') if self.galaxy_flag: - assert(isinstance(row_bounds, list) and len(row_bounds) == 2) - assert(isinstance(center_rows, list) and len(center_rows) == 2) - assert(isinstance(recon_low_pngname, str)) - assert(isinstance(recon_upp_pngname, str)) + assert(isinstance(galaxy_param, dict)) + row_bounds = galaxy_param['row_bounds'] + center_rows = galaxy_param['center_rows'] + if center_rows is None: + logging.error('Missing center_rows entry in galaxy_param') + return + center_type_selector = galaxy_param['center_type_selector'] + if center_type_selector: + if center_type_selector == 'vo': + set_center = None + elif center_type_selector == 'user': + set_center = galaxy_param['set_center'] + else: + logging.error('Illegal center_type_selector entry in galaxy_param '+ + f'({center_type_selector})') + galaxy_param['center_type_selector'] = None else: - if row_bounds: - logging.warning('Ignoring row_bounds in findCenters (only for Galaxy)') - row_bounds = None - if center_rows: - logging.warning('Ignoring center_rows in findCenters (only for Galaxy)') - center_rows = None - if recon_low_pngname: - logging.warning('Ignoring recon_low_pngname in findCenters (only for Galaxy)') - recon_low_pngname = None - if recon_upp_pngname: - logging.warning('Ignoring recon_upp_pngname in findCenters (only for Galaxy)') - recon_upp_pngname = None + if galaxy_param: + logging.warning('Ignoring galaxy_param in findCenters (only for Galaxy)') + galaxy_param = None # Check for valid available center stack index find_center = self.config.get('find_center') @@ -1610,6 +1639,15 @@ row_bounds = find_center.get('row_bounds', None) center_rows = [find_center.get('lower_row', None), find_center.get('upper_row', None)] + if row_bounds is None: + row_bounds = [0, center_stack.shape[0]] + if row_bounds[0] == -1: + row_bounds[0] = 0 + if row_bounds[1] == -1: + row_bounds[1] = center_stack.shape[0] + if not msnc.is_index_range(row_bounds, 0, center_stack.shape[0]): + msnc.illegal_value('row_bounds', row_bounds) + return # Set thetas (in degrees) theta_range = self.config['theta_range'] @@ -1687,9 +1725,10 @@ use_row = 'no' use_center = 'no' row = center_rows[0] + if self.test_mode or self.galaxy_flag: + assert(msnc.is_int(row, n1, n2-2)) if msnc.is_int(row, n1, n2-2): if self.test_mode or self.galaxy_flag: - assert(row is not None) use_row = 'yes' else: msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto') @@ -1714,9 +1753,15 @@ if self.save_plots_only: msnc.clearFig(f'theta={theta_start}') # center_stack order: row,theta,column + if galaxy_param: + recon_pngname = galaxy_param['recon_center_low'] + else: + recon_pngname = None center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg, eff_pixel_size, cross_sectional_dim, num_core=num_core, - recon_pngname=recon_low_pngname) + recon_pngname=recon_pngname, galaxy_param=galaxy_param) + logging.info(f'lower_center_offset = {center_offset:.2f} {type(center_offset)}') + print(center_offset) # Update config and save to file find_center['row_bounds'] = [n1, n2] @@ -1729,9 +1774,10 @@ use_row = 'no' use_center = 'no' row = center_rows[1] + if self.test_mode or self.galaxy_flag: + assert(msnc.is_int(row, lower_row+1, n2-1)) if msnc.is_int(row, lower_row+1, n2-1): if self.test_mode or self.galaxy_flag: - assert(row is not None) use_row = 'yes' else: msnc.quickImshow(center_stack[:,0,:], title=f'theta={theta_start}', aspect='auto') @@ -1756,10 +1802,14 @@ if self.save_plots_only: msnc.clearFig(f'theta={theta_start}') # center_stack order: row,theta,column + if galaxy_param: + recon_pngname = galaxy_param['recon_center_upp'] + else: + recon_pngname = None center_offset = self._findCenterOnePlane(center_stack[row,:,:], row, thetas_deg, eff_pixel_size, cross_sectional_dim, num_core=num_core, - recon_pngname=recon_upp_pngname) - logging.info(f'upper_center_offset = {center_offset}') + recon_pngname=recon_pngname, galaxy_param=galaxy_param) + logging.info(f'upper_center_offset = {center_offset:.2f}') del center_stack # Update config and save to file
--- a/tomo_find_center.py Wed Apr 06 19:48:22 2022 +0000 +++ b/tomo_find_center.py Thu Apr 07 21:09:58 2022 +0000 @@ -3,7 +3,6 @@ import logging import sys -import re import argparse from tomo import Tomo @@ -14,29 +13,31 @@ parser = argparse.ArgumentParser( description='Find the center axis for a tomography reconstruction') parser.add_argument('-i', '--input_stacks', - help='Preprocessed image file stacks') + required=True, help='Preprocessed image file stacks') parser.add_argument('-c', '--config', - help='Input config') + required=True, help='Input config') parser.add_argument('--row_bounds', - help='Reconstruction row bounds') + required=True, nargs=2, type=int, help='Reconstruction row bounds') parser.add_argument('--center_rows', - help='Center finding rows') + required=True, nargs=2, type=int, help='Center finding rows') + parser.add_argument('--center_type_selector', + help='Reconstruct slices for a set of center positions?') + parser.add_argument('--set_center', + type=int, help='Set center ') + parser.add_argument('--set_range', + type=float, help='Set range') + parser.add_argument('--set_step', + type=float, help='Set step') parser.add_argument('--output_config', - help='Output config') + required=True, help='Output config') parser.add_argument('--recon_center_low', - help='Lower reconstructed slice center') + help='Lower reconstructed slice center image name') parser.add_argument('--recon_center_upp', - help='Upper reconstructed slice center') + help='Upper reconstructed slice center image name') parser.add_argument('-l', '--log', - type=argparse.FileType('w'), - default=sys.stdout, - help='Log file') + type=argparse.FileType('w'), default=sys.stdout, help='Log file') args = parser.parse_args() - indexRegex = re.compile(r'\d+') - row_bounds = [int(i) for i in indexRegex.findall(args.row_bounds)] - center_rows = [int(i) for i in indexRegex.findall(args.center_rows)] - # Set basic log configuration logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' log_level = 'INFO' @@ -48,11 +49,15 @@ logging.debug(f'input_stacks = {args.input_stacks}') logging.debug(f'config = {args.config}') - logging.debug(f'row_bounds = {args.row_bounds} {row_bounds}') - logging.debug(f'center_rows = {args.center_rows} {center_rows}') + logging.debug(f'row_bounds = {args.row_bounds} {type(args.row_bounds)}') + logging.debug(f'center_rows = {args.center_rows} {type(args.center_rows)}') + logging.debug(f'center_type_selector = {args.center_type_selector}') + logging.debug(f'set_center = {args.set_center}') + logging.debug(f'set_range = {args.set_range}') + logging.debug(f'set_step = {args.set_step}') logging.debug(f'output_config = {args.output_config}') logging.debug(f'recon_center_low = {args.recon_center_low}') - logging.debug(f'recon_center_uppm = {args.recon_center_upp}') + logging.debug(f'recon_center_upp = {args.recon_center_upp}') logging.debug(f'log = {args.log}') logging.debug(f'is log stdout? {args.log is sys.stdout}') @@ -67,7 +72,11 @@ tomo.loadTomoStacks(args.input_stacks) # Find centers - tomo.findCenters(row_bounds, center_rows, args.recon_center_low, args.recon_center_upp) + galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows, + 'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center, + 'set_range' : args.set_range, 'set_step' : args.set_step, + 'recon_center_low' : args.recon_center_low, 'recon_center_upp' : args.recon_center_upp} + tomo.findCenters(galaxy_param) if __name__ == "__main__": __main__()
--- a/tomo_find_center.xml Wed Apr 06 19:48:22 2022 +0000 +++ b/tomo_find_center.xml Thu Apr 07 21:09:58 2022 +0000 @@ -1,48 +1,66 @@ -<tool id="tomo_find_center" name="Tomo Find Center Axis" version="0.1.0" python_template_version="3.9"> +<tool id="tomo_find_center" name="Tomo Find Center Axis" version="0.1.1" python_template_version="3.9"> <description>Find the center axis for a tomography reconstruction</description> - <requirements> - <requirement type="package" version="1.11.0">tomopy</requirement> - <requirement type="package" version="3.6.0">h5py</requirement> - </requirements> + <macros> + <import>tomo_macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ $__tool_directory__/tomo_find_center.py -i '$red_stacks' -c '$config' - --row_bounds '$row_bounds.row_bound_low $row_bounds.row_bound_upp' - --center_rows '$recon_centers.lower_row $recon_centers.upper_row' + --row_bounds $row_bounds.row_bound_low $row_bounds.row_bound_upp + --center_rows $recon_centers.lower_row $recon_centers.upper_row + #if str( $set.set_selector ) == "yes" + --center_type_selector '$set.center_type.center_type_selector' + #if str( $set.center_type.center_type_selector ) == "user" + --set_center '$set.center_type.set_center' + #endif + --set_range '$set.set_range' + --set_step '$set.set_step' + #endif --output_config 'output_config.yaml' --recon_center_low 'recon_center_low.png' --recon_center_upp 'recon_center_upp.png' -l '$log' ]]></command> <inputs> - <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/> - <param name="config" type='data' format='yaml' optional='false' label="Input config"/> + <expand macro="common_inputs"/> + <param name="red_stacks" type="data" format="npz" optional="false" label="Reduced stacks"/> <section name="row_bounds" title="Reconstruction row bounds"> <param name="row_bound_low" type="integer" value="-1" label="Lower bound"/> <param name="row_bound_upp" type="integer" value="-1" label="Upper bound"/> </section> <section name="recon_centers" title="Reconstruction rows to establish center axis"> - <param name="lower_row" type="integer" value="-1" label="Lower row"/> - <param name="upper_row" type="integer" value="-1" label="Upper row"/> + <param name="lower_row" type="integer" optional="false" label="Lower row"/> + <param name="upper_row" type="integer" optional="false" label="Upper row"/> </section> + <conditional name="set"> + <param name="set_selector" type="select" label="Reconstruct slices for a set of center positions?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <conditional name="center_type"> + <param name="center_type_selector" argument="--center_type_selector" type="select" label="Choose the center (C) of the set"> + <option value="vo" selected="true">Use the center obtained by Nghia Vo’s method</option> + <option value="user">Enter the center of the set</option> + </param> + <when value="user"> + <param name="set_center" argument="--set_center" type="integer" value="0" label="Center (C) of the set (0: middle of the detector row)"/> + </when> + </conditional> + <param name="set_range" argument="--set_range" type="float" value="20" label="Half-width (H) of the set ranch (in detector pixels)"/> + <param name="set_step" argument="--set_step" type="float" value="5" label="Step size (S) (in detector pixels, reconstruct slices for center at [C-H, C-H+S, ..., C+H])"/> + </when> + </conditional> </inputs> <outputs> - <data name="output_config" format="yaml" label="Output config" from_work_dir="output_config.yaml"/> - <data name="recon_center_low" format="png" label="Recontructed slice lower center" from_work_dir="recon_center_low.png"/> - <data name="recon_center_upp" format="png" label="Recontructed slice upper center" from_work_dir="recon_center_upp.png"/> - <data name="log" format="txt" label="Log"/> + <expand macro="common_outputs"/> + <data name="recon_center_low" format="png" label="Recontructed slice lower center using Nghia Vo’s method" from_work_dir="recon_center_low.png"/> + <data name="recon_center_upp" format="png" label="Recontructed slice upper center using Nghia Vo’s method" from_work_dir="recon_center_upp.png"/> </outputs> <help><![CDATA[ Preprocess tomography images. ]]></help> - <citations> - <citation type="bibtex"> -@misc{githubsum_files, - author = {Verberg, Rolf}, - year = {2022}, - title = {Tomo Find Center Axis}, -}</citation> - </citations> - + <expand macro="citations"/> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo_macros.xml Thu Apr 07 21:09:58 2022 +0000 @@ -0,0 +1,26 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.11.0">tomopy</requirement> + <requirement type="package" version="3.6.0">h5py</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> +@misc{githubsum_files, + author = {Verberg, Rolf}, + year = {2022}, + title = {Tomo Reconstruction}, +}</citation> + </citations> + </xml> + <xml name="common_inputs"> + <param name="config" type='data' format='yaml' optional='false' label="Input config"/> + </xml> + <xml name="common_outputs"> + <data name="output_config" format="yaml" label="Output config" from_work_dir="output_config.yaml"/> + <data name="log" format="txt" label="Log"/> + </xml> +</macros> +
--- a/tomo_reconstruct.xml Wed Apr 06 19:48:22 2022 +0000 +++ b/tomo_reconstruct.xml Thu Apr 07 21:09:58 2022 +0000 @@ -1,9 +1,9 @@ <tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.1.0" python_template_version="3.9"> <description>Perform a tomography reconstruction</description> - <requirements> - <requirement type="package" version="1.11.0">tomopy</requirement> - <requirement type="package" version="3.6.0">h5py</requirement> - </requirements> + <macros> + <import>tomo_macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ $__tool_directory__/tomo_reconstruct.py -i '$red_stacks' @@ -13,24 +13,15 @@ -l '$log' ]]></command> <inputs> + <expand macro="common_inputs"/> <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/> - <param name="config" type='data' format='yaml' optional='false' label="Input config"/> </inputs> <outputs> + <expand macro="common_outputs"/> <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/> - <data name="output_config" format="yaml" label="Output config" from_work_dir="output_config.yaml"/> - <data name="log" format="txt" label="Log"/> </outputs> <help><![CDATA[ Reconstruct tomography images. ]]></help> - <citations> - <citation type="bibtex"> -@misc{githubsum_files, - author = {Verberg, Rolf}, - year = {2022}, - title = {Tomo Reconstruction}, -}</citation> - </citations> - + <expand macro="citations"/> </tool>
--- a/tomo_setup.xml Wed Apr 06 19:48:22 2022 +0000 +++ b/tomo_setup.xml Thu Apr 07 21:09:58 2022 +0000 @@ -1,9 +1,9 @@ <tool id="tomo_setup" name="Tomo Setup" version="0.1.1" python_template_version="3.9"> <description>Preprocess tomography images</description> - <requirements> - <requirement type="package" version="1.11.0">tomopy</requirement> - <requirement type="package" version="3.6.0">h5py</requirement> - </requirements> + <macros> + <import>tomo_macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ cp '$inputfiles' inputfiles.txt && $__tool_directory__/tomo_setup.py @@ -29,7 +29,7 @@ ]]></configfile> </configfiles> <inputs> - <param name="config" type='data' format='yaml' optional='false' label="Input config"/> + <expand macro="common_inputs"/> <section name="thetas" title="Tomography angles"> <param name="theta_start" type="float" min="0.0" max="360.0" value="0.0" label="Lower bound"/> <param name="theta_end" type="float" min="0.0" max="360.0" value="0.0" label="Upper bound"/> @@ -42,25 +42,16 @@ </repeat> </inputs> <outputs> + <expand macro="common_outputs"/> <data name="inputfiles" format="txt" label="Input files" from_work_dir="inputfiles.txt" hidden="true"/> <data name="dark_field" format="png" label="Dark field" from_work_dir="dark_field.png"/> <data name="bright_field" format="png" label="Bright field" from_work_dir="bright_field.png"/> <data name="tomo" format="png" label="First tomography image" from_work_dir="tomo.png"/> <data name="detectorbounds" format="png" label="Detector bounds" from_work_dir="detectorbounds.png"/> <data name="output_data" format="npz" label="Preprocessed tomography data" from_work_dir="output_data.npz"/> - <data name="output_config" format="yaml" label="Output config" from_work_dir="output_config.yaml"/> - <data name="log" format="txt" label="Log"/> </outputs> <help><![CDATA[ Preprocess tomography images. ]]></help> - <citations> - <citation type="bibtex"> -@misc{githubsum_files, - author = {Verberg, Rolf}, - year = {2022}, - title = {Tomo Setup}, -}</citation> - </citations> - + <expand macro="citations"/> </tool>