imtools package¶

Test text

Subpackages¶

Submodules¶

imtools.misc module¶

imtools.qmisc module¶

imtools.sample_data module¶

imtools.sample_data.check_python_architecture(pythondir, target_arch_str)[source]¶: functions check architecture of target python

imtools.sample_data.checksum(path, hashfunc='md5')[source]¶

Return checksum given by path. Wildcards can be used in check sum. Function is strongly dependent on checksumdir package by ‘cakepietoast’.

Parameters:	path – hashfunc –
Returns:

imtools.sample_data.donut()[source]¶

Generate donut like shape with stick inside

Returns:	datap with keys data3d, segmentation and voxelsize_mm

imtools.sample_data.download_and_run(url, local_file_name)[source]¶

imtools.sample_data.downzip(url, destination='./sample_data/')[source]¶: Download, unzip and delete.

imtools.sample_data.file_copy_and_replace_lines(in_path, out_path)[source]¶

imtools.sample_data.generate(size=100, liver_intensity=100, noise_intensity=20, portal_vein_intensity=130, spleen_intensity=90)[source]¶

imtools.sample_data.get(data_label=None, destination_dir='.')[source]¶: Download sample data by data label. Labels can be listed by sample_data.data_urls.keys() :param data_label: label of data. If it is set to None, all data are downloaded :param destination_dir: output dir for data :return:

imtools.sample_data.get_conda_path()[source]¶: Return anaconda or miniconda directory :return: anaconda directory

imtools.sample_data.get_sample_data(data_label=None, destination_dir='.')[source]¶: Same as get() due to back compatibility :param data_label: :param destination_dir: :return:

imtools.sample_data.main()[source]¶

imtools.sample_data.make_icon()[source]¶

imtools.sample_data.remove(local_file_name)[source]¶

imtools.sample_data.submodule_update()[source]¶

imtools.segmentation module¶

imtools.surface_measurement module¶

Measurement of object surface.

data3d: 3D numpy array segmentation: 3D numpyarray

imtools.surface_measurement.bufford_needle_sond(data3d, voxelsize_mm, raster_mm, axis, aoi)[source]¶

imtools.surface_measurement.find_edge(segmentation, axis)[source]¶

imtools.surface_measurement.main()[source]¶

imtools.surface_measurement.surface_density(segmentation, voxelsize_mm, aoi=None, sond_raster_mm=None)[source]¶

Segmentation:	is ndarray with 0 and 1
Voxelsize_mm:	is array of three numbers specifiing size of voxel for each axis
Aoi:	is specify area of interest. It is ndarray with 0 and 1
Sond_raster_mm:	unimplemented. It is parametr of sonds design

imtools.tools module¶

imtools.uiThreshold module¶

Purpose: (CZE-ZCU-FAV-KKY) Liver medical project

Author: Pavel Volkovinsky, Miroslav Jirik Email: volkovinsky.pavel@gmail.com

Created: 2012/11/08 Copyright: (c) Pavel Volkovinsky

imtools.uiThreshold.main()[source]¶

imtools.uiThreshold.make_image_processing(data, voxelsize_mm, seeds=None, sigma_mm=1, min_threshold=None, max_threshold=None, closeNum=0, openNum=0, min_threshold_auto_method='', fill_holes=True, get_priority_objects=True, nObj=1, debug=False)[source]¶

imtools.uiThreshold.prepare_threshold_from_seeds(data, seeds, min_threshold_auto_method)[source]¶

class imtools.uiThreshold.uiThreshold(data, voxel, threshold=None, interactivity=True, number=100.0, inputSigma=-1, nObj=10, biggestObjects=True, useSeedsOfCompactObjects=True, binaryClosingIterations=2, binaryOpeningIterations=0, seeds=None, cmap=<Mock name='mock.cm.Greys_r' id='140516594474704'>, fillHoles=True, figure=None, threshold_auto_method='', threshold_upper=None, debug=True)[source]¶

UI pro prahovani 3D dat.

buttonContinue(event)[source]¶

buttonMaxNext(event)[source]¶

buttonMaxNext5(event)[source]¶

buttonMaxPrev(event)[source]¶

buttonMaxPrev5(event)[source]¶

buttonMaxUpdate(event, value)[source]¶

buttonMinNext(event)[source]¶

buttonMinNext5(event)[source]¶

buttonMinPrev(event)[source]¶

buttonMinPrev5(event)[source]¶

buttonMinUpdate(event, value)[source]¶

buttonNextClosing(event)[source]¶

buttonNextOpening(event)[source]¶

buttonPrevClosing(event)[source]¶

buttonPrevOpening(event)[source]¶

buttonReset(event)[source]¶

debugInfo()[source]¶

drawVisualization()[source]¶: Vykresleni dat.

getBiggestObjects()[source]¶: Vraceni nejvetsich objektu (nebo objektu, ktere obsahuji prioritni seedy).

returnLastThreshold()[source]¶

run()[source]¶: Spusteni UI.

updateImage(val)[source]¶: Hlavni update metoda. Cinny kod pro gaussovske filtrovani, prahovani, binarni uzavreni a otevreni a vraceni nejvetsich nebo oznacenych objektu.