Mercurial > repos > rv43 > chess_tomo
changeset 29:551d1ea2416d draft
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
| author | rv43 |
|---|---|
| date | Tue, 21 Mar 2023 18:46:02 +0000 |
| parents | 562fc79de827 |
| children | 3342c0518d4c |
| files | tomo_find_center.xml tomo_reconstruct.xml workflow/run_tomo.py |
| diffstat | 3 files changed, 80 insertions(+), 33 deletions(-) [+] |
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--- a/tomo_find_center.xml Tue Mar 21 17:59:41 2023 +0000 +++ b/tomo_find_center.xml Tue Mar 21 18:46:02 2023 +0000 @@ -11,16 +11,25 @@ --input_file "$input_file" --output_file "output.yaml" --galaxy_flag - --center_rows $center_rows.low $center_rows.upp + #if str($center_rows.type_selector) == "enter_range" + --center_rows $center_rows.low $center_rows.upp + #end if -l "$log" ]]> </command> <inputs> <param name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/> - <section name="center_rows" title="Find center axis planes"> - <param name="low" type="integer" value="-1" label="Lower bound"/> - <param name="upp" type="integer" value="-1" label="Upper bound"/> - </section> + <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="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"/>
--- a/tomo_reconstruct.xml Tue Mar 21 17:59:41 2023 +0000 +++ b/tomo_reconstruct.xml Tue Mar 21 18:46:02 2023 +0000 @@ -12,22 +12,40 @@ --center_file "$center_file" --output_file "output.nex" --galaxy_flag - --x_bounds $x_bounds.low $x_bounds.upp - --y_bounds $y_bounds.low $y_bounds.upp + #if str($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="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"/> - <section name="x_bounds" title="Boundaries of reconstructed images in x-direction"> - <param name="low" type="integer" value="-1" label="Lower bound"/> - <param name="upp" type="integer" value="-1" label="Upper bound"/> - </section> - <section name="y_bounds" title="Boundaries of reconstructed images in y-direction"> - <param name="low" type="integer" value="-1" label="Lower bound"/> - <param name="upp" type="integer" value="-1" label="Upper bound"/> - </section> + <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"/>
--- a/workflow/run_tomo.py Tue Mar 21 17:59:41 2023 +0000 +++ b/workflow/run_tomo.py Tue Mar 21 18:46:02 2023 +0000 @@ -301,14 +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 + is 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})') @@ -377,7 +381,7 @@ 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: @@ -388,7 +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) @@ -403,7 +406,7 @@ 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: @@ -513,15 +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=-1, - 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=-1, - 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: @@ -989,10 +1008,11 @@ 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] = 0 + img_x_bounds = (0, img_x_bounds[1]) if img_x_bounds[1] == -1: - img_x_bounds[1] = first_image.shape[0] + 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: