opengate.tests.utility
======================

.. py:module:: opengate.tests.utility


Attributes
----------

.. autoapisummary::

   opengate.tests.utility.plt


Classes
-------

.. autoapisummary::

   opengate.tests.utility.RootComparison


Functions
---------

.. autoapisummary::

   opengate.tests.utility.test_ok
   opengate.tests.utility.read_stat_file
   opengate.tests.utility.read_stat_file_json
   opengate.tests.utility.read_stat_file_legacy
   opengate.tests.utility.print_test
   opengate.tests.utility.assert_stats
   opengate.tests.utility.assert_stats_json
   opengate.tests.utility.plot_img_axis
   opengate.tests.utility.plot_img_z
   opengate.tests.utility.plot_img_y
   opengate.tests.utility.plot_img_x
   opengate.tests.utility.assert_images_properties
   opengate.tests.utility.assert_images
   opengate.tests.utility.plot_hist
   opengate.tests.utility.plot_profile
   opengate.tests.utility.assert_filtered_imagesprofile1D
   opengate.tests.utility.exponential_func
   opengate.tests.utility.fit_exponential_decay
   opengate.tests.utility.get_new_key_name
   opengate.tests.utility.get_keys_correspondence
   opengate.tests.utility.rel_diff
   opengate.tests.utility.rel_diff_range
   opengate.tests.utility.get_branch
   opengate.tests.utility.compare_branches
   opengate.tests.utility.compare_branches_values
   opengate.tests.utility.compare_trees
   opengate.tests.utility.get_default_test_paths
   opengate.tests.utility.compare_root2
   opengate.tests.utility.compare_root
   opengate.tests.utility.compare_root3
   opengate.tests.utility.compare_root4
   opengate.tests.utility.open_root_as_np
   opengate.tests.utility.dict_compare
   opengate.tests.utility.write_gauss_param_to_file
   opengate.tests.utility.get_gauss_param_xy
   opengate.tests.utility.extract_gauss_param_1D
   opengate.tests.utility.plot_gauss_fit
   opengate.tests.utility.create_position_vector
   opengate.tests.utility.gauss_func
   opengate.tests.utility.gaussian_fit
   opengate.tests.utility.read_mhd
   opengate.tests.utility.plot2D
   opengate.tests.utility.create_2D_Edep_colorMap
   opengate.tests.utility.compareGaussParamFromFile
   opengate.tests.utility.compareGaussParamArrays
   opengate.tests.utility.test_weights
   opengate.tests.utility.test_tps_spot_size_positions
   opengate.tests.utility.scale_dose
   opengate.tests.utility.check_dose_grid_geometry
   opengate.tests.utility.arangeDx
   opengate.tests.utility.interpolate1Dprofile
   opengate.tests.utility.getRange
   opengate.tests.utility.get_range_from_image
   opengate.tests.utility.compareRange
   opengate.tests.utility.get_1D_profile
   opengate.tests.utility.compare_dose_at_points
   opengate.tests.utility.assert_img_sum
   opengate.tests.utility.assert_images_ratio
   opengate.tests.utility.assert_images_ratio_per_voxel
   opengate.tests.utility.check_diff
   opengate.tests.utility.check_diff_abs
   opengate.tests.utility.root_compare_param_tree
   opengate.tests.utility.root_compare_param
   opengate.tests.utility.root_compare4
   opengate.tests.utility.compare_trees4
   opengate.tests.utility.get_gpu_mode_for_tests
   opengate.tests.utility.np_img_window_level
   opengate.tests.utility.np_img_crop
   opengate.tests.utility.np_plot_slice
   opengate.tests.utility.np_plot_slice_h_line
   opengate.tests.utility.np_plot_slice_v_line
   opengate.tests.utility.add_colorbar
   opengate.tests.utility.np_plot_integrated_profile
   opengate.tests.utility.np_plot_profile_X
   opengate.tests.utility.np_plot_profile_Y
   opengate.tests.utility.np_get_circle_mean_value
   opengate.tests.utility.add_circle
   opengate.tests.utility.add_border
   opengate.tests.utility.plot_compare_profile


Module Contents
---------------

.. py:data:: plt

.. py:function:: test_ok(is_ok=False)

.. py:function:: read_stat_file(filename, encoder=None)

.. py:function:: read_stat_file_json(filename)

.. py:function:: read_stat_file_legacy(filename)

.. py:function:: print_test(b, s)

.. py:function:: assert_stats(stats_actor_1, stats_actor_2, tolerance=0)

.. py:function:: assert_stats_json(stats_actor_1, stats_actor_2, tolerance=0, track_types_flag=None)

.. py:function:: plot_img_axis(ax, img, label, axis='z')

.. py:function:: plot_img_z(ax, img, label)

.. py:function:: plot_img_y(ax, img, label)

.. py:function:: plot_img_x(ax, img, label)

.. py:function:: assert_images_properties(info1, info2)

.. py:function:: assert_images(ref_filename1, filename2, stats=None, tolerance=0, ignore_value=0, axis='z', fig_name=None, sum_tolerance=5, scaleImageValuesFactor=None, sad_profile_tolerance=None)

.. py:function:: plot_hist(ax, data, label, bins=100)

.. py:function:: plot_profile(ax, y, y_spacing=1, label='')

.. py:function:: assert_filtered_imagesprofile1D(ref_filter_filename1, ref_filename1, filename2, stats=None, tolerance=0, ignore_value=0, fig_name=None, sum_tolerance=5, plt_ylim=None)

.. py:function:: exponential_func(x, a, b)

.. py:function:: fit_exponential_decay(data, start, end)

.. py:function:: get_new_key_name(key)

.. py:function:: get_keys_correspondence(keys)

.. py:function:: rel_diff(a, b)

.. py:function:: rel_diff_range(a, b)

.. py:function:: get_branch(tree, keys, key)

   Return a branch whether it is a numpy or a uproot tree


.. py:function:: compare_branches(tree1, keys1, tree2, keys2, key1, key2, tol=0.8, scaling1=1, scaling2=1, ax=False, nb_bins=200)

   Compare with Wasserstein distance
   Works well, but not easy to set the tolerance value.


.. py:function:: compare_branches_values(b1, b2, key1, key2, tol=0.8, ax=False, nb_bins=200)

   Compare with Wasserstein distance
   Works well, but not easy to set the tolerance value.


.. py:function:: compare_trees(tree1, allkeys1, tree2, allkeys2, keys1, keys2, tols, scalings1, scalings2, fig=False, nb_bins=200)

.. py:function:: get_default_test_paths(f, gate_folder=None, output_folder=None)

.. py:function:: compare_root2(root1, root2, branch1, branch2, keys, img_filename, n_tol=3)

.. py:function:: compare_root(root1, root2, branch1, branch2, checked_keys, img)

.. py:function:: compare_root3(root1, root2, branch1, branch2, keys1, keys2, tols, scalings1, scalings2, img, hits_tol=6, nb_bins=200)

.. py:function:: compare_root4(ref_root_filename, root_filename, attributes, branch1, branch2=None, img='root.png', hits_tol=6, nb_bins=200)

.. py:function:: open_root_as_np(root_file, tree_name)

.. py:function:: dict_compare(d1, d2)

.. py:function:: write_gauss_param_to_file(output_file_pathV, planePositionsV, saveFig=False)

.. py:function:: get_gauss_param_xy(data, spacing, shape, filepath=None, saveFig=False)

.. py:function:: extract_gauss_param_1D(data, length, spacing, axis=1, createFig=False)

.. py:function:: plot_gauss_fit(positionVec, dose, fit, show=False)

.. py:function:: create_position_vector(length, spacing, centered=True)

.. py:function:: gauss_func(x, A, x0, sigma)

.. py:function:: gaussian_fit(positionVec, dose)

.. py:function:: read_mhd(filename)

.. py:function:: plot2D(twodarray, label, show=False)

.. py:function:: create_2D_Edep_colorMap(filepath, show=False, axis='z')

.. py:function:: compareGaussParamFromFile(sigma, ref, rel_tol=0, abs_tol=0, verb=False)

.. py:function:: compareGaussParamArrays(paramTestV, paramRefV, rel_tol=0, abs_tol=0, verb=False)

.. py:function:: test_weights(expected_ratio, mhd_1, mhd_2, thresh=0.1)

.. py:function:: test_tps_spot_size_positions(data, ref, spacing, thresh=0.1, abs_tol=0.3)

.. py:function:: scale_dose(path, scaling, outpath='')

.. py:function:: check_dose_grid_geometry(dose_mhd_path, dose_actor)

.. py:function:: arangeDx(dx, xV, includeUB=False, lb=[], ub=[])

.. py:function:: interpolate1Dprofile(xV, dV, dx=0.01, interpolMethod='cubic')

.. py:function:: getRange(xV, dV, percentLevel=0.8)

.. py:function:: get_range_from_image(volume, shape, spacing, axis='y')

.. py:function:: compareRange(volume1, volume2, shape1, shape2, spacing1, spacing2, axis1='y', axis2='y', thresh=2.0)

.. py:function:: get_1D_profile(data, shape, spacing, axis='z')

.. py:function:: compare_dose_at_points(pointsV, dose1, dose2, shape1, shape2, spacing1, spacing2, axis1='z', axis2='z', rel_tol=0.03)

.. py:function:: assert_img_sum(img1, img2, sum_tolerance=5)

.. py:function:: assert_images_ratio(expected_ratio, mhd_1, mhd_2, abs_tolerance=0.1, fn_to_apply=None)

.. py:function:: assert_images_ratio_per_voxel(expected_ratio, mhd_1, mhd_2, abs_tolerance=0.1, mhd_is_path=True)

.. py:function:: check_diff(value1, value2, tolerance, txt)

.. py:function:: check_diff_abs(value1, value2, tolerance, txt)

.. py:function:: root_compare_param_tree(filename, tree_name, keys)

.. py:function:: root_compare_param(keys, fig)

.. py:function:: root_compare4(p1, p2, param)

   Compare two root trees.

   p1 and p2 contain = the root filename, the tree name, a list of branch names
   (see root_compare_param_tree)
   Also, each branch can be scaled and clip to a min/max range.

   param contains: the tolerance values (for all branches), the fig name,
   the nb of bins of the histograms, the tolerance for the nb of hits
   (see root_compare_param)


.. py:function:: compare_trees4(p1, p2, param)

.. py:function:: get_gpu_mode_for_tests()

   return "auto" except if the test runs with macos and github actions
   On macos and github actions, mps is detected but not usable and lead to errors.
   So we choose "cpu" in such a case


.. py:function:: np_img_window_level(img, window_width, window_level)

   Clip and rescale the grey level values of the image according to window width/level.
   Output image is within the range [0, 1]

   Parameters
   ----------
   img             an image as a numpy array
   window_width
   window_level

   Returns         the clipped and normalized image (range [0, 1])
   -------


.. py:function:: np_img_crop(img, crop_center, crop_width)

.. py:function:: np_plot_slice(ax, img, num_slice, window_width, window_level, crop_center, crop_width, spacing=(1, 1))

.. py:function:: np_plot_slice_h_line(ax, hline, crop_center, crop_width)

.. py:function:: np_plot_slice_v_line(ax, vline, crop_center, crop_width)

.. py:function:: add_colorbar(imshow, window_level, window_width)

.. py:function:: np_plot_integrated_profile(ax, img, axis, num_slice, crop_center, crop_width, label, spacing)

.. py:function:: np_plot_profile_X(ax, img, hline, num_slice, crop_center, crop_width, label, width)

.. py:function:: np_plot_profile_Y(ax, img, vline, num_slice, crop_center, crop_width, label, width)

.. py:function:: np_get_circle_mean_value(img, center, radius)

.. py:function:: add_circle(ax, img, crop_center, crop_width, center, radius)

.. py:function:: add_border(ax, border_color, border_width)

.. py:function:: plot_compare_profile(ref_names, test_names, options)

.. py:class:: RootComparison(ref_filename, filename)

   .. py:attribute:: root_ref


   .. py:attribute:: root_cmp