Mercurial > repos > rv43 > chess_tomo
changeset 33:50923144fb56 draft
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c
| author | rv43 |
|---|---|
| date | Wed, 22 Mar 2023 16:46:26 +0000 |
| parents | 98eee43a8c8c |
| children | ee2d59b83719 |
| files | __pycache__/fit.cpython-39.pyc __pycache__/general.cpython-39.pyc run_link_to_galaxy run_tomo_combine run_tomo_find_center run_tomo_reconstruct run_tomo_reduce tomo_combine.xml tomo_find_center.xml tomo_macros.xml tomo_reconstruct.xml tomo_reduce.xml workflow/__pycache__/__version__.cpython-39.pyc workflow/__pycache__/models.cpython-39.pyc workflow/__pycache__/run_tomo.cpython-39.pyc workflow/run_tomo.py |
| diffstat | 16 files changed, 140 insertions(+), 69 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_link_to_galaxy Wed Mar 22 16:46:26 2023 +0000 @@ -0,0 +1,5 @@ +#!/bin/bash + +python -m workflow link_to_galaxy -i sobhani-3249-A_start.nxs -g 'https://galaxy-dev.classe.cornell.edu' -a 'bd404baf78eef76657277f33021d408f' +python -m workflow link_to_galaxy -i tenstom_1304r-1_start.nxs -g 'https://galaxy-dev.classe.cornell.edu' -a 'bd404baf78eef76657277f33021d408f' +python -m workflow link_to_galaxy -i tenstom_1304r-1_one_stack_start.nxs -g 'https://galaxy-dev.classe.cornell.edu' -a 'bd404baf78eef76657277f33021d408f'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_tomo_combine Wed Mar 22 16:46:26 2023 +0000 @@ -0,0 +1,9 @@ +#!/bin/bash + +# From workflow +#python -m workflow run_tomo -i sobhani-3249-A_recon.nxs -o sobhani-3249-A_recon_combined.nxs -n 48 -s 'only' --combine_data +#python -m workflow run_tomo -i tenstom_1304r-1_one_stack_recon.nxs -o tenstom_1304r-1_one_stack_recon_combined.nxs -n 48 -s 'only' --combine_data +#python -m workflow run_tomo -i tenstom_1304r-1_recon.nxs -o tenstom_1304r-1_recon_combined.nxs -n 48 -s 'only' --combine_data + +# As Galaxy tool: +python tomo_combine.py -i tenstom_1304r-1_recon.nxs -o tenstom_1304r-1_recon_combined.nxs --log_level INFO -l tomo.log --galaxy_flag
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_tomo_find_center Wed Mar 22 16:46:26 2023 +0000 @@ -0,0 +1,11 @@ +#!/bin/bash + +# From workflow +#python -m workflow run_tomo -i sobhani-3249-A_reduce.nxs -o sobhani-3249-A_centers.yaml -n 48 -s 'only' --find_center +#python -m workflow run_tomo -i tenstom_1304r-1_one_stack_reduce.nxs -o tenstom_1304r-1_one_stack_centers.yaml -n 48 -s 'only' --find_center +#python -m workflow run_tomo -i tenstom_1304r-1_reduce.nxs -o tenstom_1304r-1_centers.yaml -n 48 -s 'only' --find_center + +# As Galaxy tool: +#python tomo_find_center.py -i sobhani-3249-A_reduce.nxs -o sobhani-3249-A_centers.yaml --log_level INFO -l tomo.log --galaxy_flag --center_rows 50 270 +#python tomo_find_center.py -i tenstom_1304r-1_one_stack_reduce.nxs -o tenstom_1304r-1_one_stack_centers.yaml --log_level INFO -l tomo.log --galaxy_flag --center_rows 75 850 +python tomo_find_center.py -i tenstom_1304r-1_reduce.nxs -o tenstom_1304r-1_centers.yaml --log_level INFO -l tomo.log --galaxy_flag
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_tomo_reconstruct Wed Mar 22 16:46:26 2023 +0000 @@ -0,0 +1,11 @@ +#!/bin/bash + +# From workflow +#python -m workflow run_tomo -i sobhani-3249-A_reduce.nxs -c sobhani-3249-A_centers.yaml -o sobhani-3249-A_recon.nxs -n 48 -s 'only' --reconstruct_data +#python -m workflow run_tomo -i tenstom_1304r-1_one_stack_reduce.nxs -c tenstom_1304r-1_one_stack_centers.yaml -o tenstom_1304r-1_one_stack_recon.nxs -n 48 -s 'only' --reconstruct_data +#python -m workflow run_tomo -i tenstom_1304r-1_reduce.nxs -c tenstom_1304r-1_centers.yaml -o tenstom_1304r-1_recon.nxs -n 48 -s 'only' --reconstruct_data + +# As Galaxy tool: +#python tomo_reconstruct.py -i sobhani-3249-A_reduce.nxs -c sobhani-3249-A_centers.yaml -o sobhani-3249-A_recon.nxs --log_level INFO -l tomo.log --galaxy_flag --x_bounds 650 1050 --y_bounds 270 1430 +#python tomo_reconstruct.py -i tenstom_1304r-1_one_stack_reduce.nxs -c tenstom_1304r-1_one_stack_centers.yaml -o tenstom_1304r-1_one_stack_recon.nxs --log_level INFO -l tomo.log --galaxy_flag --x_bounds 629 1450 --y_bounds 606 1468 +python tomo_reconstruct.py -i tenstom_1304r-1_reduce.nxs -c tenstom_1304r-1_centers.yaml -o tenstom_1304r-1_recon.nxs --log_level INFO -l tomo.log --galaxy_flag --x_bounds 629 1450 --y_bounds 606 1468
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_tomo_reduce Wed Mar 22 16:46:26 2023 +0000 @@ -0,0 +1,11 @@ +#!/bin/bash + +# From workflow +#python -m workflow run_tomo -i sobhani-3249-A.yaml -o sobhani-3249-A_reduce.nxs -n 48 -s 'only' --reduce_data +#python -m workflow run_tomo -i tenstom_1304r-1_one_stack.yaml -o tenstom_1304r-1_one_stack_reduce.nxs -n 48 -s 'only' --reduce_data +#python -m workflow run_tomo -i tenstom_1304r-1.yaml -o tenstom_1304r-1_reduce.nxs -n 48 -s 'only' --reduce_data + +# As Galaxy tool: +python tomo_reduce.py -i sobhani-3249-A_start.nxs -o sobhani-3249-A_reduce.nxs --log_level INFO -l tomo.log --galaxy_flag --img_x_bounds 620 950 +python tomo_reduce.py -i tenstom_1304r-1_one_stack_start.nxs -o tenstom_1304r-1_one_stack_reduce.nxs --log_level INFO -l tomo.log --galaxy_flag #--img_x_bounds 582 1509 +python tomo_reduce.py -i tenstom_1304r-1_start.nxs -o tenstom_1304r-1_reduce.nxs --log_level INFO -l tomo.log --galaxy_flag #--img_x_bounds 713 1388
--- a/tomo_combine.xml Wed Mar 22 12:56:22 2023 +0000 +++ b/tomo_combine.xml Wed Mar 22 16:46:26 2023 +0000 @@ -1,43 +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> - <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.xml Wed Mar 22 12:56:22 2023 +0000 +++ b/tomo_find_center.xml Wed Mar 22 16:46:26 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="tomo_find_center" name="Tomo Find Center Axis" version="0.3.0" 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>
--- a/tomo_macros.xml Wed Mar 22 12:56:22 2023 +0000 +++ b/tomo_macros.xml Wed Mar 22 16:46:26 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.xml Wed Mar 22 12:56:22 2023 +0000 +++ b/tomo_reconstruct.xml Wed Mar 22 16:46:26 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.3.0" 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> @@ -49,7 +49,7 @@ </inputs> <outputs> <expand macro="common_outputs"/> - <collection name="tomo_reconstruct_plots" type="list" label="Data recontructed images"> + <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_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
--- a/tomo_reduce.xml Wed Mar 22 12:56:22 2023 +0000 +++ b/tomo_reduce.xml Wed Mar 22 16:46:26 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.5" 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> @@ -19,15 +19,24 @@ </command> <inputs> <param name="input_file" type="data" optional="false" label="Input file"/> - <conditional name="img_bounds"> - <param name="type_selector" type="select" label="Choose image range for data reduction"> - <option value="full_range" selected="true">Use the full image range</option> - <option value="enter_range">Manually enter the image range</option> + <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="full_range"/> - <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 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>
--- a/workflow/run_tomo.py Wed Mar 22 12:56:22 2023 +0000 +++ b/workflow/run_tomo.py Wed Mar 22 16:46:26 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) @@ -773,7 +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 @@ -841,7 +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 @@ -856,7 +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: @@ -1069,23 +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 @@ -1145,13 +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: