Mercurial > repos > rv43 > tomo
changeset 56:ca61007a60fa draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit fc9b26da497e467c28b0adf3f94422b4cb61f59c"
| author | rv43 |
|---|---|
| date | Tue, 02 Aug 2022 19:52:47 +0000 |
| parents | bead50a4eadc |
| children | 28ea840a96f0 |
| files | general.py tomo_setup.xml |
| diffstat | 2 files changed, 173 insertions(+), 76 deletions(-) [+] |
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--- a/general.py Thu Jul 28 17:44:49 2022 +0000 +++ b/general.py Tue Aug 02 19:52:47 2022 +0000 @@ -334,6 +334,7 @@ i = input() if isinstance(i, str) and not len(i): v = default + print(f'{v}') else: v = literal_eval(i) if inset and v not in inset: @@ -389,6 +390,7 @@ i = input() if isinstance(i, str) and not len(i): v = default + print(f'{v}') else: v = literal_eval(i) except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError): @@ -460,6 +462,7 @@ i = input() if isinstance(i, str) and not len(i): i = default + print(f'{i}') if i is not None and i.lower() in 'yes': v = True elif i is not None and i.lower() in 'no': @@ -487,16 +490,25 @@ print(f'{header} (1, {len(items)}){default_string}:') for i, choice in enumerate(items): print(f' {i+1}: {choice}') - choice = input() - if isinstance(choice, str) and not len(choice): - choice = items.index(default) - else: - choice = literal_eval(choice) - if isinstance(choice, int) and 1 <= choice <= len(items): - choice -= 1 + try: + choice = input() + if isinstance(choice, str) and not len(choice): + choice = items.index(default) + print(f'{choice+1}') else: - print(f'Illegal choice, enter a number between 1 and {len(items)}') - choice = input_menu(items, default) + choice = literal_eval(choice) + if isinstance(choice, int) and 1 <= choice <= len(items): + choice -= 1 + else: + raise ValueError + except (ValueError, TypeError, SyntaxError, MemoryError, RecursionError): + choice = None + except: + print('Unexpected error') + raise + if choice is None: + print(f'Illegal choice, enter a number between 1 and {len(items)}') + choice = input_menu(items, default) return choice def create_mask(x, bounds=None, reverse_mask=False, current_mask=None): @@ -525,7 +537,7 @@ return mask def draw_mask_1d(ydata, xdata=None, current_index_ranges=None, current_mask=None, - select_mask=True, num_index_ranges_max=None, title=None, legend=None): + select_mask=True, num_index_ranges_max=None, title=None, legend=None, test_mode=False): def draw_selections(ax): ax.clear() ax.set_title(title) @@ -679,30 +691,32 @@ if current_include[-1][1] < num_data-1: current_exclude.append((current_include[-1][1]+1, num_data-1)) - # Set up matplotlib figure - plt.close('all') - fig, ax = plt.subplots() - plt.subplots_adjust(bottom=0.2) - draw_selections(ax) + if not test_mode: - # Set up event handling for click-and-drag range selection - cid_click = fig.canvas.mpl_connect('button_press_event', onclick) - cid_release = fig.canvas.mpl_connect('button_release_event', onrelease) + # Set up matplotlib figure + plt.close('all') + fig, ax = plt.subplots() + plt.subplots_adjust(bottom=0.2) + draw_selections(ax) + + # Set up event handling for click-and-drag range selection + cid_click = fig.canvas.mpl_connect('button_press_event', onclick) + cid_release = fig.canvas.mpl_connect('button_release_event', onrelease) - # Set up confirm / clear range selection buttons - confirm_b = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm') - clear_b = Button(plt.axes([0.59, 0.05, 0.15, 0.075]), 'Clear') - cid_confirm = confirm_b.on_clicked(confirm_selection) - cid_clear = clear_b.on_clicked(clear_last_selection) + # Set up confirm / clear range selection buttons + confirm_b = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm') + clear_b = Button(plt.axes([0.59, 0.05, 0.15, 0.075]), 'Clear') + cid_confirm = confirm_b.on_clicked(confirm_selection) + cid_clear = clear_b.on_clicked(clear_last_selection) - # Show figure - plt.show(block=True) + # Show figure + plt.show(block=True) - # Disconnect callbacks when figure is closed - fig.canvas.mpl_disconnect(cid_click) - fig.canvas.mpl_disconnect(cid_release) - confirm_b.disconnect(cid_confirm) - clear_b.disconnect(cid_clear) + # Disconnect callbacks when figure is closed + fig.canvas.mpl_disconnect(cid_click) + fig.canvas.mpl_disconnect(cid_release) + confirm_b.disconnect(cid_confirm) + clear_b.disconnect(cid_clear) # Swap selection depending on select_mask if not select_mask:
--- a/tomo_setup.xml Thu Jul 28 17:44:49 2022 +0000 +++ b/tomo_setup.xml Tue Aug 02 19:52:47 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="tomo_setup" name="Tomo Setup" version="0.2.0" python_template_version="3.9"> +<tool id="tomo_setup" name="Tomo Setup" version="0.2.1" python_template_version="3.9"> <description>Preprocess tomography images</description> <macros> <import>tomo_macros.xml</import> @@ -24,55 +24,136 @@ --output_config 'output_config.yaml' -l '$log' #for $s in $input.tomo_sets# ${s.offset} ${s.num} #end for + ]]> </command> <configfiles> - <configfile name="inputfiles"><![CDATA[#slurp -#if str( $input.type_selector ) == "collection" -#for $s in $input.tomo_sets -#for $input in $s.inputs -#echo str($input) + '\t' + $input.element_identifier # -#end for -#end for -#end if -]]></configfile> + <configfile name="inputfiles"> + <![CDATA[#slurp + #if str( $input.type_selector ) == "collection" + #for $s in $input.tomo_sets + #for $input in $s.inputs + #echo str($input) + '\t' + $input.element_identifier # + #end for + #end for + #end if + ]]> + </configfile> </configfiles> <inputs> - <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"/> - <param name="num_thetas" type="integer" min="1" value="1" label="Number of angles"/> - </section> - - <conditional name="input"> - <param name="type_selector" type="select" label="Choose the dataset format"> - <option value="collection">datasets as collections</option> - <option value="file">datasets as files</option> + <conditional name="config_type"> + <param name="config_selector" type="select" label="Read config from file or enter manually"> + <option value="file" selected="true">Read config from file</option> + <option value="manual">Manually enter config parameters</option> </param> - <when value="collection"> - <repeat name='tomo_sets' title="Tomography image collections"> - <param name="inputs" type="data_collection" label="Image file collection"/> - <param name="offset" type="integer" min="0" value="0" label="Image index offset"/> - <param name="num" type="integer" min="1" value="1" label="Number of images"/> - </repeat> + <when value="file"> + <expand macro="common_inputs"/> + <param name="num_stack" type="select" label="number of stacks"> + <options> + <filter type="data_meta" ref="config" key="num_stack"/> + </options> + </param> + <section name="thetas" title="Tomography angles"> + <param name="theta_start" type="select" label="Lower theta range value (from config)"> + <options> + <filter type="data_meta" ref="config" key="theta_start"/> + </options> + </param> + <param name="theta_end" type="select" label="Upper theta range value (from config)"> + <options> + <filter type="data_meta" ref="config" key="theta_end"/> + </options> + </param> + <param name="num_thetas" type="integer" min="1" value="1" optional="false" label="Number of angles"/> + </section> + <conditional name="input"> + <param name="type_selector" type="select" label="Choose the dataset format"> + <option value="collection">datasets as collections</option> + <option value="file">datasets as files</option> + </param> + <when value="collection"> + <repeat name='tomo_sets' title="Tomography image collections"> + <param name="inputs" type="data_collection" label="Image file collection"/> + <param name="offset" type="integer" min="0" value="0" label="Image index offset"/> + <param name="ref_height" type="select" label="Reference height (from config)"> + <options> + <filter type="data_meta" ref="config" key="ref_height"/> + </options> + </param> + <!-- + <param name="num" type="integer" min="1" value="1" label="Number of images"/> + --> + </repeat> + </when> + <when value="file"> + <repeat name='tomo_sets' title="Tomography image datasets"> + <conditional name="set_type"> + <param name="type_selector" type="select" label="Choose the dataset type"> + <option value="tdf">dark field</option> + <option value="tbf">bright field</option> + <option value="data">tomography field</option> + </param> + <when value="tdf"/> + <when value="tbf"/> + <when value="data"/> + </conditional> + <param name="inputs" type="data" format='h5' optional='false' label="Image file"/> + <param name="offset" type="integer" min="0" value="0" label="Image index offset"/> + <param name="ref_height" type="select" label="Reference height (from config)"> + <options> + <filter type="data_meta" ref="config" key="ref_height"/> + </options> + </param> + <!-- + <param name="num" type="integer" min="1" value="1" label="Number of images"/> + --> + </repeat> + </when> + </conditional> </when> - <when value="file"> - <repeat name='tomo_sets' title="Tomography image datasets"> - <conditional name="set_type"> - <param name="type_selector" type="select" label="Choose the dataset type"> - <option value="tdf">dark field</option> - <option value="tbf">bright field</option> - <option value="data">tomography field</option> - </param> - <when value="tdf"/> - <when value="tbf"/> - <when value="data"/> - </conditional> - <param name="inputs" type="data" format='h5' optional='false' label="Image file"/> - <param name="offset" type="integer" min="0" value="0" label="Image index offset"/> - <param name="num" type="integer" min="1" value="1" label="Number of images"/> - </repeat> + <when value="manual"> + <param name="num_stack" type="integer" min="1" value="1" label="Number of stacks"/> + <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"/> + <param name="num_thetas" type="integer" min="1" value="1" label="Number of angles"/> + </section> + <conditional name="input"> + <param name="type_selector" type="select" label="Choose the dataset format"> + <option value="collection">datasets as collections</option> + <option value="file">datasets as files</option> + </param> + <when value="collection"> + <repeat name='tomo_sets' title="Tomography image collections"> + <param name="inputs" type="data_collection" label="Image file collection"/> + <param name="offset" type="integer" min="0" value="0" label="Image index offset"/> + <param name="ref_height" type="float" value="0.0" label="Reference height"/> + <!-- + <param name="num" type="integer" min="1" value="1" label="Number of images"/> + --> + </repeat> + </when> + <when value="file"> + <repeat name='tomo_sets' title="Tomography image datasets"> + <conditional name="set_type"> + <param name="type_selector" type="select" label="Choose the dataset type"> + <option value="tdf">dark field</option> + <option value="tbf">bright field</option> + <option value="data">tomography field</option> + </param> + <when value="tdf"/> + <when value="tbf"/> + <when value="data"/> + </conditional> + <param name="inputs" type="data" format='h5' optional='false' label="Image file"/> + <param name="offset" type="integer" min="0" value="0" label="Image index offset"/> + <param name="ref_height" type="float" value="0.0" label="Reference height"/> + <!-- + <param name="num" type="integer" min="1" value="1" label="Number of images"/> + --> + </repeat> + </when> + </conditional> </when> </conditional> </inputs> @@ -87,8 +168,10 @@ <data name="output_config" format="yaml" label="Output config setup" from_work_dir="output_config.yaml"/> <data name="output_data" format="npz" label="Preprocessed tomography data" from_work_dir="output_data.npz"/> </outputs> - <help><![CDATA[ - Preprocess tomography images. - ]]></help> + <help> + <![CDATA[ + Preprocess tomography images. + ]]> + </help> <expand macro="citations"/> </tool>