Mercurial > repos > rv43 > tomo
changeset 75:d5e1d4ea2b7e draft default tip
planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
| author | rv43 |
|---|---|
| date | Thu, 23 Mar 2023 13:39:14 +0000 |
| parents | 4f4ee8db5f67 |
| children | |
| files | fit.py tomo_combine.xml tomo_find_center.py tomo_find_center.xml tomo_macros.xml tomo_reconstruct.py tomo_reconstruct.xml tomo_reduce.py tomo_reduce.xml workflow/run_tomo.py |
| diffstat | 10 files changed, 275 insertions(+), 201 deletions(-) [+] |
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--- a/fit.py Tue Mar 21 17:40:03 2023 +0000 +++ b/fit.py Thu Mar 23 13:39:14 2023 +0000 @@ -35,20 +35,18 @@ except: have_xarray = False -#try: -# from .general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \ -# almost_equal, quick_plot #, eval_expr -#except: -# try: -# from sys import path as syspath -# syspath.append(f'/nfs/chess/user/rv43/msnctools/msnctools') -# from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \ -# almost_equal, quick_plot #, eval_expr -# except: -# from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \ -# almost_equal, quick_plot #, eval_expr -from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \ - almost_equal, quick_plot #, eval_expr +try: + from .general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \ + almost_equal, quick_plot #, eval_expr +except: + try: + from sys import path as syspath + syspath.append(f'/nfs/chess/user/rv43/msnctools/msnctools') + from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \ + almost_equal, quick_plot #, eval_expr + except: + from general import illegal_value, is_int, is_dict_series, is_index, index_nearest, \ + almost_equal, quick_plot #, eval_expr from sys import float_info float_min = float_info.min
--- a/tomo_combine.xml Tue Mar 21 17:40:03 2023 +0000 +++ b/tomo_combine.xml Thu Mar 23 13:39:14 2023 +0000 @@ -1,44 +1,56 @@ -<tool id="tomo_combine" name="Tomo Combine Reconstructed Stacks" version="0.2.0" python_template_version="3.9"> +<tool id="tomo_combine" name="Tomo Combine Reconstructed Stacks" version="1.0.0" python_template_version="3.9"> <description>Combine reconstructed tomography stacks</description> <macros> <import>tomo_macros.xml</import> </macros> <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ - mkdir combine_pngs; - $__tool_directory__/tomo_combine.py - -i '$recon_stacks' - -c '$config' - --x_bounds $x_bounds.low $x_bounds.upp - --y_bounds $y_bounds.low $y_bounds.upp - --z_bounds $z_bounds.low $z_bounds.upp - --output_data 'output_data.npy' - --output_config 'output_config.yaml' - -l '$log' - ]]></command> + <command detect_errors="exit_code"> + <![CDATA[ + mkdir tomo_combine_plots; + $__tool_directory__/tomo_combine.py + --input_file "$input_file" + --output_file "output.nex" + --galaxy_flag + #if str($x_bounds.type_selector) == "enter_range" + --x_bounds $x_bounds.low $x_bounds.upp + #end if + #if str($y_bounds.type_selector) == "enter_range" + --y_bounds $y_bounds.low $y_bounds.upp + #end if + -l '$log' + ]]> + </command> <inputs> - <expand macro="common_inputs"/> - <param name="recon_stacks" type='data' format='npz' optional='false' label="Reconstructed stacks"/> - <section name="x_bounds" title="Reconstructed range in x direction"> - <param name="low" type="integer" value = "-1" label="Lower x-bound"/> - <param name="upp" type="integer" value = "-1" label="Upper x-bound"/> - </section> - <section name="y_bounds" title="Reconstructed range in y direction"> - <param name="low" type="integer" value = "-1" label="Lower y-bound"/> - <param name="upp" type="integer" value = "-1" label="Upper y-bound"/> - </section> - <section name="z_bounds" title="Reconstructed range in z direction"> - <param name="low" type="integer" value = "-1" label="Lower z-bound"/> - <param name="upp" type="integer" value = "-1" label="Upper z-bound"/> - </section> + <param name="input_file" type="data" format="nex" optional="false" label="Reconstructed tomography data"/> + <conditional name="x_bounds"> + <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction"> + <option value="full_range" selected="true">Use the full image range</option> + <option value="enter_range">Manually enter the image range</option> + </param> + <when value="full_range"/> + <when value="enter_range"> + <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/> + <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in x-direction"/> + </when> + </conditional> + <conditional name="y_bounds"> + <param name="type_selector" type="select" label="Choose reconstructed image range in y-direction"> + <option value="full_range" selected="true">Use the full image range</option> + <option value="enter_range">Manually enter the image range</option> + </param> + <when value="full_range"/> + <when value="enter_range"> + <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in y-direction"/> + <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in y-direction"/> + </when> + </conditional> </inputs> <outputs> <expand macro="common_outputs"/> - <data name="output_data" format="npy" label="Combined tomography stacks" from_work_dir="output_data.npy"/> - <collection name="combine_pngs" type="list" label="Recontructed slices midway in each combined dimension"> - <discover_datasets pattern="__name_and_ext__" directory="combine_pngs"/> + <collection name="tomo_combine_plots" type="list" label="Combine recontructed data images"> + <discover_datasets pattern="__name_and_ext__" directory="tomo_combine_plots"/> </collection> - <data name="output_config" format="tomo.config.yaml" label="Output config combine reconstruction" from_work_dir="output_config.yaml"/> + <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/> </outputs> <help><![CDATA[ Combine reconstructed tomography images.
--- a/tomo_find_center.py Tue Mar 21 17:40:03 2023 +0000 +++ b/tomo_find_center.py Thu Mar 23 13:39:14 2023 +0000 @@ -14,7 +14,7 @@ def __main__(): # Parse command line arguments parser = argparse.ArgumentParser( - description='Reduce tomography data') + description='Find the center axis for a tomography reconstruction') parser.add_argument('-i', '--input_file', required=True, type=pathlib.Path, @@ -91,5 +91,8 @@ # stopping memory monitoring # tracemalloc.stop() + logging.info('Completed find center axis') + + if __name__ == "__main__": __main__()
--- a/tomo_find_center.xml Tue Mar 21 17:40:03 2023 +0000 +++ b/tomo_find_center.xml Thu Mar 23 13:39:14 2023 +0000 @@ -1,66 +1,42 @@ -<tool id="tomo_find_center" name="Tomo Find Center Axis" version="0.2.0" python_template_version="3.9"> +<tool id="tomo_find_center" name="Tomo Find Center Axis" version="1.0.0" python_template_version="3.9"> <description>Find the center axis for a tomography reconstruction</description> <macros> <import>tomo_macros.xml</import> </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ - mkdir find_center_pngs; - $__tool_directory__/tomo_find_center.py - -i '$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 - #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' + <expand macro="requirements"/> + <command detect_errors="exit_code"> + <![CDATA[ + mkdir tomo_find_centers_plots; + $__tool_directory__/tomo_find_center.py + --input_file "$input_file" + --output_file "output.yaml" + --galaxy_flag + #if str($center_rows.type_selector) == "enter_range" + --center_rows $center_rows.low $center_rows.upp #end if - --set_range '$set.set_range' - --set_step '$set.set_step' - #end if - --output_config 'output_config.yaml' - -l '$log' - ]]></command> + -l "$log" + ]]> + </command> <inputs> - <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"/> - </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 name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/> + <conditional name="center_rows"> + <param name="type_selector" type="select" label="Choose find center axis planes"> + <option value="full_range" selected="true">Use the top and bottom image planes</option> + <option value="enter_range">Manually select the image planes</option> </param> - <when value="no"/> - <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="vo"/> - <when value="user"> - <param name="set_center" argument="--set_center" type="integer" value="0" label="Center (C) of the set in detector pixels (0: center 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 centers at [C-H, C-H+S, ..., C+H])"/> + <when value="full_range"/> + <when value="enter_range"> + <param name="low" type="integer" value="-1" optional="false" label="Lower plane index in vertical direction"/> + <param name="upp" type="integer" value="-1" optional="false" label="Upper plane index in vertical direction"/> </when> </conditional> </inputs> <outputs> <expand macro="common_outputs"/> - <collection name="find_center_pngs" type="list" label="Recontructed slices at various centers"> - <discover_datasets pattern="__name_and_ext__" directory="find_center_pngs"/> + <collection name="tomo_find_centers_plots" type="list" label="Find center images"> + <discover_datasets pattern="__name_and_ext__" directory="tomo_find_centers_plots"/> </collection> - <data name="output_config" format="tomo.config.yaml" label="Output config find center" from_work_dir="output_config.yaml"/> + <data name="output_file" format="yaml" label="Center axis info" from_work_dir="output.yaml"/> </outputs> <help><![CDATA[ Find the center axis for a tomography reconstruction.
--- a/tomo_macros.xml Tue Mar 21 17:40:03 2023 +0000 +++ b/tomo_macros.xml Thu Mar 23 13:39:14 2023 +0000 @@ -10,19 +10,13 @@ <xml name="citations"> <citations> <citation type="bibtex"> -@misc{github_files, +@misc{chess_tomography, author = {Verberg, Rolf}, - year = {2022}, + year = {2023}, title = {Tomo Reconstruction}, }</citation> </citations> </xml> - <!-- - <xml name="common_inputs"> - <param name="config" type='data' format='yaml' optional='false' label="Input config"/> - <param name="config" type='data' format='tomo.config.yaml' optional='true' label="Input config"/> - </xml> - --> <xml name="common_outputs"> <data name="log" format="txt" label="Log"/> </xml>
--- a/tomo_reconstruct.py Tue Mar 21 17:40:03 2023 +0000 +++ b/tomo_reconstruct.py Thu Mar 23 13:39:14 2023 +0000 @@ -14,7 +14,7 @@ def __main__(): # Parse command line arguments parser = argparse.ArgumentParser( - description='Reduce tomography data') + description='Perform a tomography reconstruction') parser.add_argument('-i', '--input_file', required=True, type=pathlib.Path, @@ -106,5 +106,8 @@ # stopping memory monitoring # tracemalloc.stop() + logging.info('Completed tomography reconstruction') + + if __name__ == "__main__": __main__()
--- a/tomo_reconstruct.xml Tue Mar 21 17:40:03 2023 +0000 +++ b/tomo_reconstruct.xml Thu Mar 23 13:39:14 2023 +0000 @@ -1,43 +1,58 @@ -<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.2.0" python_template_version="3.9"> +<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="1.0.0" python_template_version="3.9"> <description>Perform a tomography reconstruction</description> <macros> <import>tomo_macros.xml</import> </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ - mkdir center_slice_pngs; - $__tool_directory__/tomo_reconstruct.py - -i '$red_stacks' - -c '$config' - #if str($center_offsets.type_selector) == "offsets_manual" - --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset - #end if - --output_data 'output_data.npz' - --output_config 'output_config.yaml' - -l '$log' - ]]></command> + <expand macro="requirements"/> + <command detect_errors="exit_code"> + <![CDATA[ + mkdir tomo_reconstruct_plots; + $__tool_directory__/tomo_reconstruct.py + --input_file "$input_file" + --center_file "$center_file" + --output_file "output.nex" + --galaxy_flag + #if str($x_bounds.type_selector) == "enter_range" + --x_bounds $x_bounds.low $x_bounds.upp + #end if + #if str($y_bounds.type_selector) == "enter_range" + --y_bounds $y_bounds.low $y_bounds.upp + #end if + -l "$log" + ]]> + </command> <inputs> - <expand macro="common_inputs"/> - <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/> - <conditional name="center_offsets"> - <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually"> - <option value="offsets_from_file" selected="true">Read center axis offsets from file</option> - <option value="offsets_manual">Manually enter center axis offsets</option> + <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/> + <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/> + <conditional name="x_bounds"> + <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction"> + <option value="full_range" selected="true">Use the full image range</option> + <option value="enter_range">Manually enter the image range</option> </param> - <when value="offsets_from_file"/> - <when value="offsets_manual"> - <param name="lower_center_offset" type="float" value = "0" optional="false" label="Lower center offset"/> - <param name="upper_center_offset" type="float" value = "0" optional="false" label="Upper center offset"/> + <when value="full_range"/> + <when value="enter_range"> + <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/> + <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in x-direction"/> + </when> + </conditional> + <conditional name="y_bounds"> + <param name="type_selector" type="select" label="Choose reconstructed image range in y-direction"> + <option value="full_range" selected="true">Use the full image range</option> + <option value="enter_range">Manually enter the image range</option> + </param> + <when value="full_range"/> + <when value="enter_range"> + <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in y-direction"/> + <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in y-direction"/> </when> </conditional> </inputs> <outputs> <expand macro="common_outputs"/> - <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/> - <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension"> - <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/> + <collection name="tomo_reconstruct_plots" type="list" label="Data recontruction images"> + <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/> </collection> - <data name="output_config" format="tomo.config.yaml" label="Output config reconstruction" from_work_dir="output_config.yaml"/> + <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/> </outputs> <help><![CDATA[ Reconstruct tomography images.
--- a/tomo_reduce.py Tue Mar 21 17:40:03 2023 +0000 +++ b/tomo_reduce.py Thu Mar 23 13:39:14 2023 +0000 @@ -18,7 +18,7 @@ parser.add_argument('-i', '--input_file', required=True, type=pathlib.Path, - help='''Full or relative path to the input file (in yaml or nxs format).''') + help='''Full or relative path to the input file (in yaml or Nexus format).''') parser.add_argument('-o', '--output_file', required=True, type=pathlib.Path, @@ -92,5 +92,8 @@ # Stop memory monitoring # tracemalloc.stop() + logging.info('Completed tomography data reduction') + + if __name__ == "__main__": __main__()
--- a/tomo_reduce.xml Tue Mar 21 17:40:03 2023 +0000 +++ b/tomo_reduce.xml Thu Mar 23 13:39:14 2023 +0000 @@ -1,29 +1,53 @@ -<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.0" python_template_version="3.9"> +<tool id="tomo_reduce" name="Tomo Reduce" version="1.0.0" python_template_version="3.9"> <description>Reduce tomography images</description> <macros> <import>tomo_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"/> <command detect_errors="exit_code"> <![CDATA[ mkdir tomo_reduce_plots; $__tool_directory__/tomo_reduce.py - --input_file '$input_file' - --output_file 'output.nxs' + --input_file "$input_file" + --output_file "output.nex" --galaxy_flag - --img_x_bounds $x_bounds.x_bound_low $x_bounds.x_bound_upp - -l '$log' + #if str($station.type_selector) == "id3b" + #if str($station.img_bounds.type_selector) == "enter_range" + --img_x_bounds $station.img_bounds.low $station.img_bounds.upp + #end if + #end if + -l "$log" ]]> </command> <inputs> <param name="input_file" type="data" optional="false" label="Input file"/> + <conditional name="station"> + <param name="type_selector" type="select" display="radio" label="Choose station"> + <option value="id3a" selected="true">id3a (SMB)</option> + <option value="id3b">id3b (FMB)</option> + </param> + <when value="id3a"/> + <when value="id3b"> + <conditional name="img_bounds"> + <param name="type_selector" type="select" display="radio" label="Choose image range for data reduction"> + <option value="enter_range" selected="true">Manually enter the image range</option> + <option value="full_range">Use the full image range</option> + </param> + <when value="enter_range"> + <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in vertical direction"/> + <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in vertical direction"/> + </when> + <when value="full_range"/> + </conditional> + </when> + </conditional> </inputs> <outputs> <expand macro="common_outputs"/> - <collection name="tomo_reduce_plots" type="list" label="Tomo data reduction images"> + <collection name="tomo_reduce_plots" type="list" label="Data reduction images"> <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/> </collection> - <data name="output_file" format="nxs" label="Reduced tomography data" from_work_dir="output.nxs"/> + <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/> </outputs> <help> <![CDATA[
--- a/workflow/run_tomo.py Tue Mar 21 17:40:03 2023 +0000 +++ b/workflow/run_tomo.py Thu Mar 23 13:39:14 2023 +0000 @@ -15,7 +15,7 @@ from multiprocessing import cpu_count from nexusformat.nexus import * -from os import mkdir +from os import mkdir, environ from os import path as os_path try: from skimage.transform import iradon @@ -99,7 +99,7 @@ self.num_core = num_core def __enter__(self): - self.num_core_org = ne.set_num_threads(self.num_core) + self.num_core_org = ne.set_num_threads(min(self.num_core, ne.MAX_THREADS)) def __exit__(self, exc_type, exc_value, traceback): ne.set_num_threads(self.num_core_org) @@ -164,28 +164,42 @@ self.num_core= cpu_count() def read(self, filename): - extension = os_path.splitext(filename)[1] - if extension == '.yml' or extension == '.yaml': - with open(filename, 'r') as f: - config = safe_load(f) -# if len(config) > 1: -# raise ValueError(f'Multiple root entries in {filename} not yet implemented') -# if len(list(config.values())[0]) > 1: -# raise ValueError(f'Multiple sample maps in {filename} not yet implemented') - return(config) - elif extension == '.nxs': - with NXFile(filename, mode='r') as nxfile: - nxroot = nxfile.readfile() - return(nxroot) + logger.info(f'looking for {filename}') + if self.galaxy_flag: + try: + with open(filename, 'r') as f: + config = safe_load(f) + return(config) + except: + try: + with NXFile(filename, mode='r') as nxfile: + nxroot = nxfile.readfile() + return(nxroot) + except: + raise ValueError(f'Unable to open ({filename})') else: - raise ValueError(f'Invalid filename extension ({extension})') + extension = os_path.splitext(filename)[1] + if extension == '.yml' or extension == '.yaml': + with open(filename, 'r') as f: + config = safe_load(f) +# if len(config) > 1: +# raise ValueError(f'Multiple root entries in {filename} not yet implemented') +# if len(list(config.values())[0]) > 1: +# raise ValueError(f'Multiple sample maps in {filename} not yet implemented') + return(config) + elif extension == '.nxs': + with NXFile(filename, mode='r') as nxfile: + nxroot = nxfile.readfile() + return(nxroot) + else: + raise ValueError(f'Invalid filename extension ({extension})') def write(self, data, filename): extension = os_path.splitext(filename)[1] if extension == '.yml' or extension == '.yaml': with open(filename, 'w') as f: safe_dump(data, f) - elif extension == '.nxs': + elif extension == '.nxs' or extension == '.nex': data.save(filename, mode='w') elif extension == '.nc': data.to_netcdf(os_path=filename) @@ -287,14 +301,18 @@ nxentry = nxroot[nxroot.attrs['default']] if not isinstance(nxentry, NXentry): raise ValueError(f'Invalid nxentry ({nxentry})') - if self.galaxy_flag: - if center_rows is not None: - center_rows = tuple(center_rows) - if not is_int_pair(center_rows): + if center_rows is not None: + if self.galaxy_flag: + if not is_int_pair(center_rows, ge=-1): raise ValueError(f'Invalid parameter center_rows ({center_rows})') - elif center_rows is not None: - logger.warning(f'Ignoring parameter center_rows ({center_rows})') - center_rows = None + if (center_rows[0] != -1 and center_rows[1] != -1 and + center_rows[0] > center_rows[1]): + center_rows = (center_rows[1], center_rows[0]) + else: + center_rows = tuple(center_rows) + else: + logger.warning(f'Ignoring parameter center_rows ({center_rows})') + center_rows = None if self.galaxy_flag: if center_stack_index is not None and not is_int(center_stack_index, ge=0): raise ValueError(f'Invalid parameter center_stack_index ({center_stack_index})') @@ -360,10 +378,10 @@ if self.test_mode: lower_row = self.test_config['lower_row'] elif self.galaxy_flag: - if center_rows is None: + if center_rows is None or center_rows[0] == -1: lower_row = 0 else: - lower_row = min(center_rows) + lower_row = center_rows[0] if not 0 <= lower_row < tomo_fields_shape[2]-1: raise ValueError(f'Invalid parameter center_rows ({center_rows})') else: @@ -374,7 +392,6 @@ logger.debug('Finding center...') t0 = time() lower_center_offset = self._find_center_one_plane( - #np.asarray(nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:]), nxentry.reduced_data.data.tomo_fields[center_stack_index,:,lower_row,:], lower_row, thetas, eff_pixel_size, cross_sectional_dim, path=path, num_core=self.num_core) @@ -386,10 +403,10 @@ if self.test_mode: upper_row = self.test_config['upper_row'] elif self.galaxy_flag: - if center_rows is None: + if center_rows is None or center_rows[1] == -1: upper_row = tomo_fields_shape[2]-1 else: - upper_row = max(center_rows) + upper_row = center_rows[1] if not lower_row < upper_row < tomo_fields_shape[2]: raise ValueError(f'Invalid parameter center_rows ({center_rows})') else: @@ -499,15 +516,31 @@ # Resize the reconstructed tomography data # reconstructed data order in each stack: row/z,x,y if self.test_mode: - x_bounds = self.test_config.get('x_bounds') - y_bounds = self.test_config.get('y_bounds') + x_bounds = tuple(self.test_config.get('x_bounds')) + y_bounds = tuple(self.test_config.get('y_bounds')) z_bounds = None elif self.galaxy_flag: - if x_bounds is not None and not is_int_pair(x_bounds, ge=0, - lt=tomo_recon_stacks[0].shape[1]): + x_max = tomo_recon_stacks[0].shape[1] + if x_bounds is None: + x_bounds = (0, x_max) + elif is_int_pair(x_bounds, ge=-1, le=x_max): + x_bounds = tuple(x_bounds) + if x_bounds[0] == -1: + x_bounds = (0, x_bounds[1]) + if x_bounds[1] == -1: + x_bounds = (x_bounds[0], x_max) + if not is_index_range(x_bounds, ge=0, le=x_max): raise ValueError(f'Invalid parameter x_bounds ({x_bounds})') - if y_bounds is not None and not is_int_pair(y_bounds, ge=0, - lt=tomo_recon_stacks[0].shape[1]): + y_max = tomo_recon_stacks[0].shape[1] + if y_bounds is None: + y_bounds = (0, y_max) + elif is_int_pair(y_bounds, ge=-1, le=y_max): + y_bounds = tuple(y_bounds) + if y_bounds[0] == -1: + y_bounds = (0, y_bounds[1]) + if y_bounds[1] == -1: + y_bounds = (y_bounds[0], y_max) + if not is_index_range(y_bounds, ge=0, le=y_max): raise ValueError(f'Invalid parameter y_bounds ({y_bounds})') z_bounds = None else: @@ -535,17 +568,17 @@ if num_tomo_stacks == 1: basetitle = 'recon' else: - basetitle = f'recon stack {i+1}' + basetitle = f'recon stack' for i, stack in enumerate(tomo_recon_stacks): - title = f'{basetitle} {res_title} xslice{x_slice}' + title = f'{basetitle} {i+1} {res_title} xslice{x_slice}' quick_imshow(stack[z_range[0]:z_range[1],x_slice,y_range[0]:y_range[1]], title=title, path=path, save_fig=self.save_figs, save_only=self.save_only, block=self.block) - title = f'{basetitle} {res_title} yslice{y_slice}' + title = f'{basetitle} {i+1} {res_title} yslice{y_slice}' quick_imshow(stack[z_range[0]:z_range[1],x_range[0]:x_range[1],y_slice], title=title, path=path, save_fig=self.save_figs, save_only=self.save_only, block=self.block) - title = f'{basetitle} {res_title} zslice{z_slice}' + title = f'{basetitle} {i+1} {res_title} zslice{z_slice}' quick_imshow(stack[z_slice,x_range[0]:x_range[1],y_range[0]:y_range[1]], title=title, path=path, save_fig=self.save_figs, save_only=self.save_only, block=self.block) @@ -740,7 +773,7 @@ # Take median if tdf_stack.ndim == 2: - tdf = tdf_stack + tdf = tdf_stack.astype('float64') elif tdf_stack.ndim == 3: tdf = np.median(tdf_stack, axis=0) del tdf_stack @@ -808,7 +841,7 @@ We don’t typically account for them but potentially could. """ if tbf_stack.ndim == 2: - tbf = tbf_stack + tbf = tbf_stack.astype('float64') elif tbf_stack.ndim == 3: tbf = np.median(tbf_stack, axis=0) del tbf_stack @@ -823,7 +856,7 @@ # Set any non-positive values to one # (avoid negative bright field values for spikes in dark field) - tbf[tbf < 1] = 1 + tbf[tbf < 1.0] = 1.0 # Plot bright field if self.galaxy_flag: @@ -873,9 +906,6 @@ # Select image bounds title = f'tomography image at theta={round(theta, 2)+0}' - if (img_x_bounds is not None and not is_index_range(img_x_bounds, ge=0, - le=first_image.shape[0])): - raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})') if nxentry.instrument.source.attrs['station'] in ('id1a3', 'id3a'): pixel_size = nxentry.instrument.detector.x_pixel_size # Try to get a fit from the bright field @@ -977,6 +1007,14 @@ if self.galaxy_flag: if img_x_bounds is None: img_x_bounds = (0, first_image.shape[0]) + elif is_int_pair(img_x_bounds, ge=-1, le=first_image.shape[0]): + img_x_bounds = tuple(img_x_bounds) + if img_x_bounds[0] == -1: + img_x_bounds = (0, img_x_bounds[1]) + if img_x_bounds[1] == -1: + img_x_bounds = (img_x_bounds[0], first_image.shape[0]) + if not is_index_range(img_x_bounds, ge=0, le=first_image.shape[0]): + raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})') else: quick_imshow(first_image, title=title) print('Select vertical data reduction range from first tomography image') @@ -1031,23 +1069,29 @@ """ # Get full bright field tbf = np.asarray(reduced_data.data.bright_field) - tbf_shape = tbf.shape + img_shape = tbf.shape # Get image bounds - img_x_bounds = tuple(reduced_data.get('img_x_bounds', (0, tbf_shape[0]))) - img_y_bounds = tuple(reduced_data.get('img_y_bounds', (0, tbf_shape[1]))) + img_x_bounds = tuple(reduced_data.get('img_x_bounds', (0, img_shape[0]))) + img_y_bounds = tuple(reduced_data.get('img_y_bounds', (0, img_shape[1]))) + if img_x_bounds == (0, img_shape[0]) and img_y_bounds == (0, img_shape[1]): + resize_flag = False + else: + resize_flag = True # Get resized dark field -# if 'dark_field' in data: -# tbf = np.asarray(reduced_data.data.dark_field[ -# img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]) -# else: -# logger.warning('Dark field unavailable') -# tdf = None - tdf = None + if 'dark_field' in reduced_data.data: + if resize_flag: + tdf = np.asarray(reduced_data.data.dark_field[ + img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]]) + else: + tdf = np.asarray(reduced_data.data.dark_field) + else: + logger.warning('Dark field unavailable') + tdf = None # Resize bright field - if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]): + if resize_flag: tbf = tbf[img_x_bounds[0]:img_x_bounds[1],img_y_bounds[0]:img_y_bounds[1]] # Get the tomography images @@ -1107,13 +1151,15 @@ else: path = self.output_folder for i, tomo_stack in enumerate(tomo_stacks): - # Resize the tomography images - # Right now the range is the same for each set in the image stack. - if img_x_bounds != (0, tbf.shape[0]) or img_y_bounds != (0, tbf.shape[1]): + # Resize the tomography images as needed + # Right now the range is the same for each set in the image stack + if resize_flag: t0 = time() tomo_stack = tomo_stack[:,img_x_bounds[0]:img_x_bounds[1], img_y_bounds[0]:img_y_bounds[1]].astype('float64') logger.debug(f'Resizing tomography images took {time()-t0:.2f} seconds') + else: + tomo_stack = tomo_stack.astype('float64') # Subtract dark field if tdf is not None: