mia_processes.utils package

Utilities and tools used across mia_processes

Contains:

Modules:

• report.py

• tools.py

Submodules

mia_processes.utils.report module

Module dedicated to report generation

Contains:

Class:

• Report

class mia_processes.utils.report.Report(report_file, dict4runtime, **kwargs)

Bases: object

Create pdf report

In the constructor, certain kwarg keys will specialise the report:

• CVR: CVR report

• GE2REC: GE2REC report

• IQMs_file: MRIQC individual report (with all IQMs)

• mriqc_group: MRIQC report group

• Perf_DSC: DSC perfusion report

Methods:

• co2_inhal_cvr_make_report

• ge2rec_make_report

• get_iqms_data

• mriqc_anat_make_report

• mriqc_func_make_report

• mriqc_group_make_report

• perf_dsc_make_report

__init__(report_file, dict4runtime, **kwargs)

Create Canvas , create cover and make report

co2_inhal_cvr_make_report()

Make CVR under CO2 challenge report

ge2rec_make_report()

Make GE2REC report

get_iqms_data(param)

Get iqms data

mriqc_anat_make_report()

Make mriqc anat individual report

mriqc_func_make_report()

Make mriqc functional individual report

mriqc_group_make_report()

Make mriqc group report

perf_dsc_make_report()

Make DSC MR perfusion report

mia_processes.utils.tools module

Module that contains multiple functions used across mia_processes

Contains:

Class:

• PageNumCanvas

• ReportLine

Functions:

• checkFileExt

• del_dbFieldValue

• dict4runtime_update

• get_dbFieldValue

• mriqc_get_all_run

• mriqc_group_iqms_tsv

• plot_boxplot_points

• plot_qi2

• plot_segmentation

• plot_slice_planes

• plot_realignment_parameters

• set_dbFieldValue

class mia_processes.utils.tools.PageNumCanvas(*args, **kwargs)

Bases: Canvas

For add “page number of total” in each footer.

__init__(*args, **kwargs)

Constructor.

draw_page_number(page_count)

Add the page number.

save()

Add the page number to each page (page x of y).

showPage()

On a page break, add information to the list.

class mia_processes.utils.tools.ReportLine(width, height=0)

Bases: Flowable

Line flowable — draws a line in a flowable

__init__(width, height=0)

draw()

Draw the line

mia_processes.utils.tools.checkFileExt(in_file, ext_dic)

Check file extension

Parameters:

• in_file – file name (a string)

• ext_dic – dictionary of the valid extensions for the file (dictionary, ex: EXT = {‘NIFTI_GZ’: ‘nii.gz’, ‘NIFTI’: ‘nii’})

Returns:

• valid_bool: True if extension is valid (a boolean)

• in_ext: file extension (a string)

• file_name: file name without extension (a string)

mia_processes.utils.tools.check_orientations(images, verbose=True)

Check the dimensions and orientations of the images.

images: images from nibabel verbose: whether to create a verbose returned message.

returns: status: status (True means OK)

message: string describing status (empty if OK)

mia_processes.utils.tools.del_dbFieldValue(project, document, tags2del)

Delete for a document, the value for a field in the db.

Parameters:

• project – the project.

• document – the absolute path of the document.

• tag_to_del – a list of fields where values will be deleted

mia_processes.utils.tools.dict4runtime_update(dict4runtime, database, db_filename, *args)

Update the dict4runtime dictionary object with tags values

Parameters:

• dict4runtime – the dict used in mia_processes bricks to pass data from the list_outputs method to the run_process_mia method

• database – the database object (for example: self.project.session)

• db_filename – the name of the database file from which the tag value will be retrieved

• args – the tags to be recovered

mia_processes.utils.tools.get_dbFieldValue(project, document, field)

Return, for a document, the field value from the database.

Parameters:

• project – the project.

• document – the absolute path of the document.

• field – the field name.

Returns:

the value of the field for the document in the database.

mia_processes.utils.tools.mriqc_get_all_run(modality, project, output_directory)

Get all raw files name with a mriqc run for one project and for one modality.

Parameters:

• modality – modality (a string, ‘bold’ or ‘anat’)

• project – the project (Project Object)

• output_directory – output directory where all json files are stored (a string that representing a path)

Returns:

• files_names (a list)

mia_processes.utils.tools.mriqc_group_iqms_tsv(modality, output_directory)

Get all IQMs from mriqc json report for one project and for one modality and put them together in one tsv file.

Parameters:

• modality – modality (a string, ‘bold’ or ‘anat’)

• output_directory – output directory where all json files are stored (a string that representing a path)

Returns:

• dataframe: all IQMs in a panda dataframe

• out_tsv: out tsv file (a string that representing a file)

mia_processes.utils.tools.plot_boxplot_points(dataframe, title, ylabel, out_file=None)

Plot boxplot with points data and save the figure in a png image

Parameters:

• dataframe – tabular data (a pandas dataframe)

• title – figure title (a string)

• ylabel – y axis label (a string)

• out_file – out figure path (a string)

Returns:

• out_file: out figure path (a string)

mia_processes.utils.tools.plot_qi2(x_grid, ref_pdf, fit_pdf, ref_data, cutoff_idx, out_file=None)

bla bla

mia_processes.utils.tools.plot_realignment_parameters(realignment_parameters, vox_size, out_file_tra, out_file_rot, figsize=(12, 5.6))

Plot SPM realignment parameters.

Parameters:

• realignment_parameters – realignment parameters file (a string representing an existing file) or realignment parameters (a numpy.ndarray object with shape[1] == 6)

• vox_size – voxel size of the data (a list of 3 float or integer)

• out_file_tra – out path for the translation figure (a string representing a path file)

• out_file_rot – out path for the rotation figure (a string representing a path file)

• figsize – width, height of parametric maps plot, in inches (float, float)

Returns:

• qc: result of the quality check (a boolean). True: OK

mia_processes.utils.tools.plot_segmentation(anat_file, segmentation, name, out_dir=None, **kwargs)

Adapted from <https://github.com/nipreps/mriqc/blob/5a0f0408bd0c176dbc46088c6ffe279269180f3f/mriqc/viz/utils.py#L550>

mia_processes.utils.tools.plot_slice_planes(data_1, data_2=None, plane='ax', fig_rows=4, fig_cols=4, slice_start=None, slice_step=None, dyn=1, cmap_1='Greys_r', vmin_1=None, vmax_1=None, cmap_2='rainbow', vmin_2=None, vmax_2=None, out_dir=None, only_noise=False, out_name=None)

Create a PNG file with a mosaic display of volume slices.

Several images can be overlaid. data_1, the only mandatory argument, is the background image (or the only image displayed). data_2 is the image (or images) superimposed on data_1.

fig_rows, fig_cols, slice_start and slice_step are optional. If they are not known, plot_slice_planes will try to adapt as best it can to obtain an acceptable display. The default values for fig_rows, fig_cols and dyn are 4, 4 and 1 respectively.

Parameters:

• data_1 – an existing, image file (valid extensions: .nii).

• data_2 – an existing, image file or a list of existing image files (valid extensions: .nii).

• plane – orientation plane (ax, sag or cor)

• fig_rows – the number of rows in the images panel (integer).

• fig_cols – the number of columns in the images panel (integer).

• slice_start – starting slice number to be displayed (integer).

• slice_step – the gap between each slice to be displayed (integer).

• dyn – the volume number in the space-time, for 4D (integer).

• cmap_1 – the color map name (string) for data_1.

• vmin_1 – the low value of the range used for data_1 display(float).

• vmax_1 – the high value of the range used for data_1 display(float).

• cmap_2 – the color map name (string) or a list of RGB tuple (ex. [(255, 0, 0), (0, 0, 255)]).

• vmin_2 – the low value of the range used for data_2 display(float).

• vmax_2 – the high value of the range used for data_2 display(float).

• out_dir – the output directory where the mosaic images will be saved.

• only_noise – if True, shows the noise (boolean).

• out_name – the suffix added to form the output name (string).

Note: cmap for parametric display can be, gist_rainbow, RdYlBu, Spectral,

rainbow_r, jet_r, seismic_r, bwr_r

mia_processes.utils.tools.set_dbFieldValue(project, document, tag_to_add)

Creates for a document, the field and the corresponding value in the db.

Parameters:

• project – the project.

• document – the absolute path of the document.

• tag_to_add – a dictionary with ‘default_value’, ‘description’, ‘field_type’, ‘name’, ‘origin’, ‘unit’, ‘value’, ‘visibility’ keys.