def _run(input_saliency_file_name, input_gradcam_file_name,
input_bwo_file_name, input_novelty_file_name, max_percentile_level,
radar_channel_idx_for_thres, threshold_value, threshold_type_string,
output_file_name):
"""Runs probability-matched means (PMM).
This is effectively the main method.
:param input_saliency_file_name: See documentation at top of file.
:param input_gradcam_file_name: Same.
:param input_bwo_file_name: Same.
:param input_novelty_file_name: Same.
:param max_percentile_level: Same.
:param radar_channel_idx_for_thres: Same.
:param threshold_value: Same.
:param threshold_type_string: Same.
:param output_file_name: Same.
"""
if input_saliency_file_name not in NONE_STRINGS:
input_gradcam_file_name = None
input_bwo_file_name = None
input_novelty_file_name = None
elif input_gradcam_file_name not in NONE_STRINGS:
input_saliency_file_name = None
input_bwo_file_name = None
input_novelty_file_name = None
elif input_bwo_file_name not in NONE_STRINGS:
input_saliency_file_name = None
input_gradcam_file_name = None
input_novelty_file_name = None
else:
input_saliency_file_name = None
input_gradcam_file_name = None
input_bwo_file_name = None
if radar_channel_idx_for_thres < 0:
radar_channel_idx_for_thres = None
threshold_value = None
threshold_type_string = None
if input_saliency_file_name is not None:
print('Reading data from: "{0:s}"...'.format(input_saliency_file_name))
saliency_dict = saliency_maps.read_standard_file(
input_saliency_file_name)
list_of_input_matrices = saliency_dict[
saliency_maps.INPUT_MATRICES_KEY]
elif input_gradcam_file_name is not None:
print('Reading data from: "{0:s}"...'.format(input_gradcam_file_name))
gradcam_dict = gradcam.read_standard_file(input_gradcam_file_name)
list_of_input_matrices = gradcam_dict[gradcam.INPUT_MATRICES_KEY]
elif input_bwo_file_name is not None:
print('Reading data from: "{0:s}"...'.format(input_bwo_file_name))
bwo_dictionary = backwards_opt.read_standard_file(input_bwo_file_name)
list_of_input_matrices = bwo_dictionary[
backwards_opt.INIT_FUNCTION_KEY]
else:
print('Reading data from: "{0:s}"...'.format(input_novelty_file_name))
novelty_dict = novelty_detection.read_standard_file(
input_novelty_file_name)
list_of_input_matrices = novelty_dict[
novelty_detection.TRIAL_INPUTS_KEY]
novel_indices = novelty_dict[novelty_detection.NOVEL_INDICES_KEY]
list_of_input_matrices = [
a[novel_indices, ...] for a in list_of_input_matrices
]
print('Running PMM on denormalized predictor matrices...')
num_input_matrices = len(list_of_input_matrices)
list_of_mean_input_matrices = [None] * num_input_matrices
pmm_metadata_dict = None
threshold_count_matrix = None
for i in range(num_input_matrices):
if i == 0:
list_of_mean_input_matrices[i], threshold_count_matrix = (
pmm.run_pmm_many_variables(
input_matrix=list_of_input_matrices[i],
max_percentile_level=max_percentile_level,
threshold_var_index=radar_channel_idx_for_thres,
threshold_value=threshold_value,
threshold_type_string=threshold_type_string))
pmm_metadata_dict = pmm.check_input_args(
input_matrix=list_of_input_matrices[i],
max_percentile_level=max_percentile_level,
threshold_var_index=radar_channel_idx_for_thres,
threshold_value=threshold_value,
threshold_type_string=threshold_type_string)
else:
list_of_mean_input_matrices[i] = pmm.run_pmm_many_variables(
input_matrix=list_of_input_matrices[i],
max_percentile_level=max_percentile_level)[0]
if input_saliency_file_name is not None:
print('Running PMM on saliency matrices...')
list_of_saliency_matrices = saliency_dict[
saliency_maps.SALIENCY_MATRICES_KEY]
num_input_matrices = len(list_of_input_matrices)
list_of_mean_saliency_matrices = [None] * num_input_matrices
for i in range(num_input_matrices):
list_of_mean_saliency_matrices[i] = pmm.run_pmm_many_variables(
input_matrix=list_of_saliency_matrices[i],
max_percentile_level=max_percentile_level)[0]
print('Writing output to: "{0:s}"...'.format(output_file_name))
saliency_maps.write_pmm_file(
pickle_file_name=output_file_name,
list_of_mean_input_matrices=list_of_mean_input_matrices,
list_of_mean_saliency_matrices=list_of_mean_saliency_matrices,
threshold_count_matrix=threshold_count_matrix,
model_file_name=saliency_dict[saliency_maps.MODEL_FILE_KEY],
standard_saliency_file_name=input_saliency_file_name,
pmm_metadata_dict=pmm_metadata_dict)
return
if input_gradcam_file_name is not None:
print('Running PMM on class-activation matrices...')
list_of_cam_matrices = gradcam_dict[gradcam.CAM_MATRICES_KEY]
list_of_guided_cam_matrices = gradcam_dict[
gradcam.GUIDED_CAM_MATRICES_KEY]
num_input_matrices = len(list_of_input_matrices)
list_of_mean_cam_matrices = [None] * num_input_matrices
list_of_mean_guided_cam_matrices = [None] * num_input_matrices
for i in range(num_input_matrices):
if list_of_cam_matrices[i] is None:
continue
list_of_mean_cam_matrices[i] = pmm.run_pmm_many_variables(
input_matrix=numpy.expand_dims(list_of_cam_matrices[i],
axis=-1),
max_percentile_level=max_percentile_level)[0]
list_of_mean_cam_matrices[i] = list_of_mean_cam_matrices[i][..., 0]
list_of_mean_guided_cam_matrices[i] = pmm.run_pmm_many_variables(
input_matrix=list_of_guided_cam_matrices[i],
max_percentile_level=max_percentile_level)[0]
print('Writing output to: "{0:s}"...'.format(output_file_name))
gradcam.write_pmm_file(
pickle_file_name=output_file_name,
list_of_mean_input_matrices=list_of_mean_input_matrices,
list_of_mean_cam_matrices=list_of_mean_cam_matrices,
list_of_mean_guided_cam_matrices=list_of_mean_guided_cam_matrices,
model_file_name=gradcam_dict[gradcam.MODEL_FILE_KEY],
standard_gradcam_file_name=input_gradcam_file_name,
pmm_metadata_dict=pmm_metadata_dict)
return
if input_bwo_file_name is not None:
print('Running PMM on backwards-optimization output...')
list_of_optimized_matrices = bwo_dictionary[
backwards_opt.OPTIMIZED_MATRICES_KEY]
num_input_matrices = len(list_of_input_matrices)
list_of_mean_optimized_matrices = [None] * num_input_matrices
for i in range(num_input_matrices):
list_of_mean_optimized_matrices[i] = pmm.run_pmm_many_variables(
input_matrix=list_of_optimized_matrices[i],
max_percentile_level=max_percentile_level)[0]
mean_initial_activation = numpy.mean(
bwo_dictionary[backwards_opt.INITIAL_ACTIVATIONS_KEY])
mean_final_activation = numpy.mean(
bwo_dictionary[backwards_opt.FINAL_ACTIVATIONS_KEY])
print('Writing output to: "{0:s}"...'.format(output_file_name))
backwards_opt.write_pmm_file(
pickle_file_name=output_file_name,
list_of_mean_input_matrices=list_of_mean_input_matrices,
list_of_mean_optimized_matrices=list_of_mean_optimized_matrices,
mean_initial_activation=mean_initial_activation,
mean_final_activation=mean_final_activation,
threshold_count_matrix=threshold_count_matrix,
model_file_name=bwo_dictionary[backwards_opt.MODEL_FILE_KEY],
standard_bwo_file_name=input_bwo_file_name,
pmm_metadata_dict=pmm_metadata_dict)
return
print('Running PMM on novelty-detection output...')
mean_novel_image_matrix_upconv = pmm.run_pmm_many_variables(
input_matrix=novelty_dict[novelty_detection.NOVEL_IMAGES_UPCONV_KEY],
max_percentile_level=max_percentile_level)[0]
mean_novel_image_matrix_upconv_svd = pmm.run_pmm_many_variables(
input_matrix=novelty_dict[
novelty_detection.NOVEL_IMAGES_UPCONV_SVD_KEY],
max_percentile_level=max_percentile_level)[0]
print('Writing output to: "{0:s}"...'.format(output_file_name))
novelty_detection.write_pmm_file(
pickle_file_name=output_file_name,
mean_novel_image_matrix=list_of_mean_input_matrices[0],
mean_novel_image_matrix_upconv=mean_novel_image_matrix_upconv,
mean_novel_image_matrix_upconv_svd=mean_novel_image_matrix_upconv_svd,
threshold_count_matrix=threshold_count_matrix,
standard_novelty_file_name=input_novelty_file_name,
pmm_metadata_dict=pmm_metadata_dict)
def _run(input_file_name, allow_whitespace, plot_significance,
plot_regions_of_interest, colour_map_name, max_colour_percentile,
top_output_dir_name):
"""Plots Grad-CAM output (class-activation maps).
This is effectively the main method.
:param input_file_name: See documentation at top of file.
:param allow_whitespace: Same.
:param plot_significance: Same.
:param plot_regions_of_interest: Same.
:param colour_map_name: Same.
:param max_colour_percentile: Same.
:param top_output_dir_name: Same.
"""
if plot_significance:
plot_regions_of_interest = False
unguided_cam_dir_name = '{0:s}/main_gradcam'.format(top_output_dir_name)
guided_cam_dir_name = '{0:s}/guided_gradcam'.format(top_output_dir_name)
file_system_utils.mkdir_recursive_if_necessary(
directory_name=unguided_cam_dir_name)
file_system_utils.mkdir_recursive_if_necessary(
directory_name=guided_cam_dir_name)
# Check input args.
error_checking.assert_is_geq(max_colour_percentile, 0.)
error_checking.assert_is_leq(max_colour_percentile, 100.)
colour_map_object = pyplot.cm.get_cmap(colour_map_name)
print('Reading data from: "{0:s}"...'.format(input_file_name))
try:
gradcam_dict = gradcam.read_standard_file(input_file_name)
list_of_input_matrices = gradcam_dict[gradcam.INPUT_MATRICES_KEY]
list_of_cam_matrices = gradcam_dict[gradcam.CAM_MATRICES_KEY]
list_of_guided_cam_matrices = gradcam_dict[
gradcam.GUIDED_CAM_MATRICES_KEY]
full_storm_id_strings = gradcam_dict[gradcam.FULL_IDS_KEY]
storm_times_unix_sec = gradcam_dict[gradcam.STORM_TIMES_KEY]
except ValueError:
gradcam_dict = gradcam.read_pmm_file(input_file_name)
list_of_input_matrices = gradcam_dict[gradcam.MEAN_INPUT_MATRICES_KEY]
list_of_cam_matrices = gradcam_dict[gradcam.MEAN_CAM_MATRICES_KEY]
list_of_guided_cam_matrices = gradcam_dict[
gradcam.MEAN_GUIDED_CAM_MATRICES_KEY]
for i in range(len(list_of_input_matrices)):
list_of_input_matrices[i] = numpy.expand_dims(
list_of_input_matrices[i], axis=0)
if list_of_cam_matrices[i] is None:
continue
list_of_cam_matrices[i] = numpy.expand_dims(
list_of_cam_matrices[i], axis=0)
list_of_guided_cam_matrices[i] = numpy.expand_dims(
list_of_guided_cam_matrices[i], axis=0)
full_storm_id_strings = [None]
storm_times_unix_sec = [None]
pmm_flag = (full_storm_id_strings[0] is None
and storm_times_unix_sec[0] is None)
# Read metadata for CNN.
model_file_name = gradcam_dict[gradcam.MODEL_FILE_KEY]
model_metafile_name = '{0:s}/model_metadata.p'.format(
os.path.split(model_file_name)[0])
print(
'Reading model metadata from: "{0:s}"...'.format(model_metafile_name))
model_metadata_dict = cnn.read_model_metadata(model_metafile_name)
print(SEPARATOR_STRING)
cam_monte_carlo_dict = (gradcam_dict[gradcam.CAM_MONTE_CARLO_KEY]
if plot_significance else None)
guided_cam_monte_carlo_dict = (
gradcam_dict[gradcam.GUIDED_CAM_MONTE_CARLO_KEY]
if plot_significance else None)
region_dict = (gradcam_dict[gradcam.REGION_DICT_KEY]
if plot_regions_of_interest else None)
num_examples = list_of_input_matrices[0].shape[0]
num_input_matrices = len(list_of_input_matrices)
for i in range(num_examples):
these_figure_objects, these_axes_object_matrices = (
plot_input_examples.plot_one_example(
list_of_predictor_matrices=list_of_input_matrices,
model_metadata_dict=model_metadata_dict,
plot_sounding=False,
allow_whitespace=allow_whitespace,
pmm_flag=pmm_flag,
example_index=i,
full_storm_id_string=full_storm_id_strings[i],
storm_time_unix_sec=storm_times_unix_sec[i]))
for j in range(num_input_matrices):
if list_of_cam_matrices[j] is None:
continue
if cam_monte_carlo_dict is None:
this_significance_matrix = None
else:
this_significance_matrix = numpy.logical_or(
cam_monte_carlo_dict[
monte_carlo.TRIAL_PMM_MATRICES_KEY][j][i, ...] <
cam_monte_carlo_dict[monte_carlo.MIN_MATRICES_KEY][j][i,
...],
cam_monte_carlo_dict[
monte_carlo.TRIAL_PMM_MATRICES_KEY][j][i, ...] >
cam_monte_carlo_dict[monte_carlo.MAX_MATRICES_KEY][j][i,
...])
this_num_spatial_dim = len(list_of_input_matrices[j].shape) - 2
if this_num_spatial_dim == 3:
_plot_3d_radar_cam(
colour_map_object=colour_map_object,
max_colour_percentile=max_colour_percentile,
figure_objects=these_figure_objects,
axes_object_matrices=these_axes_object_matrices,
model_metadata_dict=model_metadata_dict,
output_dir_name=unguided_cam_dir_name,
cam_matrix=list_of_cam_matrices[j][i, ...],
significance_matrix=this_significance_matrix,
full_storm_id_string=full_storm_id_strings[i],
storm_time_unix_sec=storm_times_unix_sec[i])
else:
if region_dict is None:
_plot_2d_radar_cam(
colour_map_object=colour_map_object,
max_colour_percentile=max_colour_percentile,
figure_objects=these_figure_objects,
axes_object_matrices=these_axes_object_matrices,
model_metadata_dict=model_metadata_dict,
output_dir_name=unguided_cam_dir_name,
cam_matrix=list_of_cam_matrices[j][i, ...],
significance_matrix=this_significance_matrix,
full_storm_id_string=full_storm_id_strings[i],
storm_time_unix_sec=storm_times_unix_sec[i])
else:
_plot_2d_regions(
figure_objects=these_figure_objects,
axes_object_matrices=these_axes_object_matrices,
model_metadata_dict=model_metadata_dict,
list_of_polygon_objects=region_dict[
gradcam.POLYGON_OBJECTS_KEY][j][i],
output_dir_name=unguided_cam_dir_name,
full_storm_id_string=full_storm_id_strings[i],
storm_time_unix_sec=storm_times_unix_sec[i])
these_figure_objects, these_axes_object_matrices = (
plot_input_examples.plot_one_example(
list_of_predictor_matrices=list_of_input_matrices,
model_metadata_dict=model_metadata_dict,
plot_sounding=False,
allow_whitespace=allow_whitespace,
pmm_flag=pmm_flag,
example_index=i,
full_storm_id_string=full_storm_id_strings[i],
storm_time_unix_sec=storm_times_unix_sec[i]))
for j in range(num_input_matrices):
if list_of_guided_cam_matrices[j] is None:
continue
if guided_cam_monte_carlo_dict is None:
this_significance_matrix = None
else:
this_significance_matrix = numpy.logical_or(
guided_cam_monte_carlo_dict[
monte_carlo.TRIAL_PMM_MATRICES_KEY][j][i, ...] <
guided_cam_monte_carlo_dict[monte_carlo.MIN_MATRICES_KEY]
[j][i, ...], guided_cam_monte_carlo_dict[
monte_carlo.TRIAL_PMM_MATRICES_KEY][j][i, ...] >
guided_cam_monte_carlo_dict[
monte_carlo.MAX_MATRICES_KEY][j][i, ...])
this_num_spatial_dim = len(list_of_input_matrices[j].shape) - 2
if this_num_spatial_dim == 3:
_plot_3d_radar_cam(
colour_map_object=colour_map_object,
max_colour_percentile=max_colour_percentile,
figure_objects=these_figure_objects,
axes_object_matrices=these_axes_object_matrices,
model_metadata_dict=model_metadata_dict,
output_dir_name=guided_cam_dir_name,
guided_cam_matrix=list_of_guided_cam_matrices[j][i, ...],
significance_matrix=this_significance_matrix,
full_storm_id_string=full_storm_id_strings[i],
storm_time_unix_sec=storm_times_unix_sec[i])
else:
_plot_2d_radar_cam(
colour_map_object=colour_map_object,
max_colour_percentile=max_colour_percentile,
figure_objects=these_figure_objects,
axes_object_matrices=these_axes_object_matrices,
model_metadata_dict=model_metadata_dict,
output_dir_name=guided_cam_dir_name,
guided_cam_matrix=list_of_guided_cam_matrices[j][i, ...],
significance_matrix=this_significance_matrix,
full_storm_id_string=full_storm_id_strings[i],
storm_time_unix_sec=storm_times_unix_sec[i])
def _run(interpretation_type_string, baseline_file_name, trial_file_name,
max_pmm_percentile_level, num_iterations, confidence_level,
output_file_name):
"""Runs Monte Carlo significance test for interpretation output.
This is effectively the main method.
:param interpretation_type_string: See documentation at top of file.
:param baseline_file_name: Same.
:param trial_file_name: Same.
:param max_pmm_percentile_level: Same.
:param num_iterations: Same.
:param confidence_level: Same.
:param output_file_name: Same.
:raises: ValueError: if
`interpretation_type_string not in VALID_INTERPRETATION_TYPE_STRINGS`.
"""
if interpretation_type_string not in VALID_INTERPRETATION_TYPE_STRINGS:
error_string = (
'\n{0:s}\nValid interpretation types (listed above) do not include '
'"{1:s}".'
).format(
str(VALID_INTERPRETATION_TYPE_STRINGS), interpretation_type_string
)
raise ValueError(error_string)
print('Reading baseline set from: "{0:s}"...'.format(baseline_file_name))
if interpretation_type_string == SALIENCY_STRING:
baseline_dict = saliency_maps.read_standard_file(baseline_file_name)
elif interpretation_type_string == GRADCAM_STRING:
baseline_dict = gradcam.read_standard_file(baseline_file_name)
else:
baseline_dict = backwards_opt.read_standard_file(baseline_file_name)
print('Reading trial set from: "{0:s}"...'.format(trial_file_name))
monte_carlo_dict = None
cam_monte_carlo_dict = None
guided_cam_monte_carlo_dict = None
if interpretation_type_string == SALIENCY_STRING:
trial_dict = saliency_maps.read_standard_file(trial_file_name)
monte_carlo_dict = monte_carlo.run_monte_carlo_test(
list_of_baseline_matrices=baseline_dict[
saliency_maps.SALIENCY_MATRICES_KEY],
list_of_trial_matrices=trial_dict[
saliency_maps.SALIENCY_MATRICES_KEY],
max_pmm_percentile_level=max_pmm_percentile_level,
num_iterations=num_iterations, confidence_level=confidence_level)
monte_carlo_dict[monte_carlo.BASELINE_FILE_KEY] = baseline_file_name
list_of_input_matrices = trial_dict[saliency_maps.INPUT_MATRICES_KEY]
elif interpretation_type_string == GRADCAM_STRING:
trial_dict = gradcam.read_standard_file(trial_file_name)
cam_monte_carlo_dict = monte_carlo.run_monte_carlo_test(
list_of_baseline_matrices=baseline_dict[gradcam.CAM_MATRICES_KEY],
list_of_trial_matrices=trial_dict[gradcam.CAM_MATRICES_KEY],
max_pmm_percentile_level=max_pmm_percentile_level,
num_iterations=num_iterations, confidence_level=confidence_level)
guided_cam_monte_carlo_dict = monte_carlo.run_monte_carlo_test(
list_of_baseline_matrices=baseline_dict[
gradcam.GUIDED_CAM_MATRICES_KEY],
list_of_trial_matrices=trial_dict[
gradcam.GUIDED_CAM_MATRICES_KEY],
max_pmm_percentile_level=max_pmm_percentile_level,
num_iterations=num_iterations, confidence_level=confidence_level)
cam_monte_carlo_dict[
monte_carlo.BASELINE_FILE_KEY] = baseline_file_name
guided_cam_monte_carlo_dict[
monte_carlo.BASELINE_FILE_KEY] = baseline_file_name
list_of_input_matrices = trial_dict[gradcam.INPUT_MATRICES_KEY]
else:
trial_dict = backwards_opt.read_standard_file(trial_file_name)
monte_carlo_dict = monte_carlo.run_monte_carlo_test(
list_of_baseline_matrices=baseline_dict[
backwards_opt.OPTIMIZED_MATRICES_KEY],
list_of_trial_matrices=trial_dict[
backwards_opt.OPTIMIZED_MATRICES_KEY],
max_pmm_percentile_level=max_pmm_percentile_level,
num_iterations=num_iterations, confidence_level=confidence_level)
monte_carlo_dict[monte_carlo.BASELINE_FILE_KEY] = baseline_file_name
list_of_input_matrices = trial_dict[backwards_opt.INIT_FUNCTION_KEY]
print(SEPARATOR_STRING)
num_matrices = len(list_of_input_matrices)
list_of_mean_input_matrices = [None] * num_matrices
for i in range(num_matrices):
list_of_mean_input_matrices[i] = pmm.run_pmm_many_variables(
input_matrix=list_of_input_matrices[i],
max_percentile_level=max_pmm_percentile_level
)[0]
pmm_metadata_dict = pmm.check_input_args(
input_matrix=list_of_input_matrices[0],
max_percentile_level=max_pmm_percentile_level,
threshold_var_index=None, threshold_value=None,
threshold_type_string=None)
print('Writing results to: "{0:s}"...'.format(output_file_name))
if interpretation_type_string == SALIENCY_STRING:
saliency_maps.write_pmm_file(
pickle_file_name=output_file_name,
list_of_mean_input_matrices=list_of_mean_input_matrices,
list_of_mean_saliency_matrices=copy.deepcopy(
monte_carlo_dict[monte_carlo.TRIAL_PMM_MATRICES_KEY]
),
threshold_count_matrix=None,
model_file_name=trial_dict[saliency_maps.MODEL_FILE_KEY],
standard_saliency_file_name=trial_file_name,
pmm_metadata_dict=pmm_metadata_dict,
monte_carlo_dict=monte_carlo_dict)
elif interpretation_type_string == GRADCAM_STRING:
gradcam.write_pmm_file(
pickle_file_name=output_file_name,
list_of_mean_input_matrices=list_of_mean_input_matrices,
list_of_mean_cam_matrices=copy.deepcopy(
cam_monte_carlo_dict[monte_carlo.TRIAL_PMM_MATRICES_KEY]
),
list_of_mean_guided_cam_matrices=copy.deepcopy(
guided_cam_monte_carlo_dict[monte_carlo.TRIAL_PMM_MATRICES_KEY]
),
model_file_name=trial_dict[gradcam.MODEL_FILE_KEY],
standard_gradcam_file_name=trial_file_name,
pmm_metadata_dict=pmm_metadata_dict,
cam_monte_carlo_dict=cam_monte_carlo_dict,
guided_cam_monte_carlo_dict=guided_cam_monte_carlo_dict)
else:
backwards_opt.write_pmm_file(
pickle_file_name=output_file_name,
list_of_mean_input_matrices=list_of_mean_input_matrices,
list_of_mean_optimized_matrices=copy.deepcopy(
monte_carlo_dict[monte_carlo.TRIAL_PMM_MATRICES_KEY]
),
mean_initial_activation=numpy.mean(
trial_dict[backwards_opt.INITIAL_ACTIVATIONS_KEY]
),
mean_final_activation=numpy.mean(
trial_dict[backwards_opt.FINAL_ACTIVATIONS_KEY]
),
threshold_count_matrix=None,
model_file_name=trial_dict[backwards_opt.MODEL_FILE_KEY],
standard_bwo_file_name=trial_file_name,
pmm_metadata_dict=pmm_metadata_dict,
monte_carlo_dict=monte_carlo_dict)
def _run(input_gradcam_file_name, percentile_threshold, min_class_activation,
output_file_name):
"""Thresholds Grad-CAM output to create regions of interest (polygons).
This is effectively the main method.
:param input_gradcam_file_name: See documentation at top of file.
:param percentile_threshold: Same.
:param min_class_activation: Same.
:param output_file_name: Same.
:raises: TypeError: if any class-activation map contains not-2 spatial
dimensions.
"""
error_checking.assert_is_geq(percentile_threshold, 50.)
error_checking.assert_is_less_than(percentile_threshold, 100.)
error_checking.assert_is_greater(min_class_activation, 0.)
print('Reading data from: "{0:s}"...\n'.format(input_gradcam_file_name))
pmm_flag = False
try:
gradcam_dict = gradcam.read_standard_file(input_gradcam_file_name)
list_of_cam_matrices = gradcam_dict.pop(gradcam.CAM_MATRICES_KEY)
except ValueError:
gradcam_dict = gradcam.read_pmm_file(input_gradcam_file_name)
list_of_cam_matrices = gradcam_dict.pop(gradcam.MEAN_CAM_MATRICES_KEY)
for j in range(len(list_of_cam_matrices)):
if list_of_cam_matrices[j] is None:
continue
list_of_cam_matrices[j] = numpy.expand_dims(
list_of_cam_matrices[j], axis=0
)
pmm_flag = True
num_matrices = len(list_of_cam_matrices)
num_examples = None
for j in range(num_matrices):
if list_of_cam_matrices[j] is None:
continue
num_examples = list_of_cam_matrices[j].shape[0]
this_num_spatial_dim = len(list_of_cam_matrices[j].shape) - 1
if this_num_spatial_dim == 2:
continue
error_string = (
'This script deals with only 2-D class-activation maps. {0:d}th '
'input matrix contains {1:d} spatial dimensions.'
).format(j + 1, this_num_spatial_dim)
raise TypeError(error_string)
list_of_mask_matrices = [None] * num_matrices
list_of_polygon_objects = [[[] * 0] * num_examples] * num_matrices
for i in range(num_examples):
for j in range(num_matrices):
if list_of_cam_matrices[j] is None:
continue
this_min_class_activation = numpy.percentile(
list_of_cam_matrices[j][i, ...], percentile_threshold
)
this_min_class_activation = max([
this_min_class_activation, min_class_activation
])
print((
'Creating mask for {0:d}th example and {1:d}th class-activation'
' matrix, with threshold = {2:.3e}...'
).format(
i + 1, j + 1, this_min_class_activation
))
this_mask_matrix = (
list_of_cam_matrices[j][i, ...] >= this_min_class_activation
)
print('{0:d} of {1:d} grid points are inside mask.\n'.format(
numpy.sum(this_mask_matrix.astype(int)), this_mask_matrix.size
))
list_of_polygon_objects[j][i] = _mask_to_polygons(this_mask_matrix)
this_mask_matrix = numpy.expand_dims(this_mask_matrix, axis=0)
if list_of_mask_matrices[j] is None:
list_of_mask_matrices[j] = copy.deepcopy(this_mask_matrix)
else:
list_of_mask_matrices[j] = numpy.concatenate(
(list_of_mask_matrices[j], this_mask_matrix), axis=0
)
if pmm_flag:
for j in range(len(list_of_mask_matrices)):
if list_of_mask_matrices[j] is None:
continue
list_of_mask_matrices[j] = list_of_mask_matrices[j][0, ...]
region_dict = {
gradcam.MASK_MATRICES_KEY: list_of_mask_matrices,
gradcam.POLYGON_OBJECTS_KEY: list_of_polygon_objects,
gradcam.PERCENTILE_THRESHOLD_KEY: percentile_threshold,
gradcam.MIN_CLASS_ACTIVATION_KEY: min_class_activation
}
if output_file_name in ['', 'None']:
output_file_name = input_gradcam_file_name
print('Writing regions of interest to: "{0:s}"...'.format(output_file_name))
gradcam.add_regions_to_file(
input_file_name=input_gradcam_file_name,
output_file_name=output_file_name, region_dict=region_dict)
def _run(input_human_file_name, input_machine_file_name, guided_gradcam_flag,
abs_percentile_threshold, output_dir_name):
"""Compares human-generated vs. machine-generated interpretation map.
This is effectively the main method.
:param input_human_file_name: See documentation at top of file.
:param input_machine_file_name: Same.
:param guided_gradcam_flag: Same.
:param abs_percentile_threshold: Same.
:param output_dir_name: Same.
"""
file_system_utils.mkdir_recursive_if_necessary(
directory_name=output_dir_name)
if abs_percentile_threshold < 0:
abs_percentile_threshold = None
if abs_percentile_threshold is not None:
error_checking.assert_is_leq(abs_percentile_threshold, 100.)
print('Reading data from: "{0:s}"...'.format(input_human_file_name))
human_polygon_dict = human_polygons.read_polygons(input_human_file_name)
human_positive_mask_matrix_4d = human_polygon_dict[
human_polygons.POSITIVE_MASK_MATRIX_KEY]
human_negative_mask_matrix_4d = human_polygon_dict[
human_polygons.NEGATIVE_MASK_MATRIX_KEY]
full_storm_id_string = human_polygon_dict[human_polygons.STORM_ID_KEY]
storm_time_unix_sec = human_polygon_dict[human_polygons.STORM_TIME_KEY]
pmm_flag = full_storm_id_string is None and storm_time_unix_sec is None
print('Reading data from: "{0:s}"...'.format(input_machine_file_name))
# TODO(thunderhoser): This is a HACK.
machine_channel_indices = numpy.array([2, 8], dtype=int)
if pmm_flag:
try:
saliency_dict = saliency_maps.read_pmm_file(input_machine_file_name)
saliency_flag = True
model_file_name = saliency_dict[saliency_maps.MODEL_FILE_KEY]
predictor_matrix = saliency_dict.pop(
saliency_maps.MEAN_INPUT_MATRICES_KEY
)[0][..., machine_channel_indices]
machine_interpretation_matrix_3d = saliency_dict.pop(
saliency_maps.MEAN_SALIENCY_MATRICES_KEY
)[0][..., machine_channel_indices]
except ValueError:
gradcam_dict = gradcam.read_pmm_file(input_machine_file_name)
saliency_flag = False
model_file_name = gradcam_dict[gradcam.MODEL_FILE_KEY]
predictor_matrix = gradcam_dict.pop(
gradcam.MEAN_INPUT_MATRICES_KEY
)[0][..., machine_channel_indices]
if guided_gradcam_flag:
machine_interpretation_matrix_3d = gradcam_dict.pop(
gradcam.MEAN_GUIDED_GRADCAM_KEY
)[..., machine_channel_indices]
else:
machine_interpretation_matrix_3d = gradcam_dict.pop(
gradcam.MEAN_CLASS_ACTIVATIONS_KEY)
else:
try:
saliency_dict = saliency_maps.read_standard_file(
input_machine_file_name)
saliency_flag = True
all_full_id_strings = saliency_dict[saliency_maps.FULL_IDS_KEY]
all_times_unix_sec = saliency_dict[saliency_maps.STORM_TIMES_KEY]
model_file_name = saliency_dict[saliency_maps.MODEL_FILE_KEY]
predictor_matrix = saliency_dict.pop(
saliency_maps.INPUT_MATRICES_KEY
)[0][..., machine_channel_indices]
machine_interpretation_matrix_3d = saliency_dict.pop(
saliency_maps.SALIENCY_MATRICES_KEY
)[0][..., machine_channel_indices]
except ValueError:
gradcam_dict = gradcam.read_standard_file(input_machine_file_name)
saliency_flag = False
all_full_id_strings = gradcam_dict[gradcam.FULL_IDS_KEY]
all_times_unix_sec = gradcam_dict[gradcam.STORM_TIMES_KEY]
model_file_name = gradcam_dict[gradcam.MODEL_FILE_KEY]
predictor_matrix = gradcam_dict.pop(
gradcam.INPUT_MATRICES_KEY
)[0][..., machine_channel_indices]
if guided_gradcam_flag:
machine_interpretation_matrix_3d = gradcam_dict.pop(
gradcam.GUIDED_GRADCAM_KEY
)[..., machine_channel_indices]
else:
machine_interpretation_matrix_3d = gradcam_dict.pop(
gradcam.CLASS_ACTIVATIONS_KEY)
storm_object_index = tracking_utils.find_storm_objects(
all_id_strings=all_full_id_strings,
all_times_unix_sec=all_times_unix_sec,
id_strings_to_keep=[full_storm_id_string],
times_to_keep_unix_sec=numpy.array(
[storm_time_unix_sec], dtype=int
),
allow_missing=False
)[0]
predictor_matrix = predictor_matrix[storm_object_index, ...]
machine_interpretation_matrix_3d = machine_interpretation_matrix_3d[
storm_object_index, ...]
if not saliency_flag and not guided_gradcam_flag:
machine_interpretation_matrix_3d = numpy.expand_dims(
machine_interpretation_matrix_3d, axis=-1)
machine_interpretation_matrix_3d = numpy.repeat(
a=machine_interpretation_matrix_3d,
repeats=predictor_matrix.shape[-1], axis=-1)
if not (saliency_flag or guided_gradcam_flag):
human_negative_mask_matrix_4d = None
model_metafile_name = '{0:s}/model_metadata.p'.format(
os.path.split(model_file_name)[0]
)
print('Reading metadata from: "{0:s}"...'.format(model_metafile_name))
model_metadata_dict = cnn.read_model_metadata(model_metafile_name)
model_metadata_dict[cnn.LAYER_OPERATIONS_KEY] = [
model_metadata_dict[cnn.LAYER_OPERATIONS_KEY][k]
for k in machine_channel_indices
]
human_positive_mask_matrix_3d, human_negative_mask_matrix_3d = (
_reshape_human_maps(
model_metadata_dict=model_metadata_dict,
positive_mask_matrix_4d=human_positive_mask_matrix_4d,
negative_mask_matrix_4d=human_negative_mask_matrix_4d)
)
num_channels = human_positive_mask_matrix_3d.shape[-1]
machine_positive_mask_matrix_3d = numpy.full(
human_positive_mask_matrix_3d.shape, False, dtype=bool)
positive_iou_by_channel = numpy.full(num_channels, numpy.nan)
if human_negative_mask_matrix_3d is None:
machine_negative_mask_matrix_3d = None
negative_iou_by_channel = None
else:
machine_negative_mask_matrix_3d = numpy.full(
human_negative_mask_matrix_3d.shape, False, dtype=bool)
negative_iou_by_channel = numpy.full(num_channels, numpy.nan)
for k in range(num_channels):
this_negative_matrix = (
None if human_negative_mask_matrix_3d is None
else human_negative_mask_matrix_3d[..., k]
)
this_comparison_dict = _do_comparison_one_channel(
machine_interpretation_matrix_2d=machine_interpretation_matrix_3d[
..., k],
abs_percentile_threshold=abs_percentile_threshold,
human_positive_mask_matrix_2d=human_positive_mask_matrix_3d[..., k],
human_negative_mask_matrix_2d=this_negative_matrix)
machine_positive_mask_matrix_3d[..., k] = this_comparison_dict[
MACHINE_POSITIVE_MASK_KEY]
positive_iou_by_channel[k] = this_comparison_dict[POSITIVE_IOU_KEY]
if human_negative_mask_matrix_3d is None:
continue
machine_negative_mask_matrix_3d[..., k] = this_comparison_dict[
MACHINE_NEGATIVE_MASK_KEY]
negative_iou_by_channel[k] = this_comparison_dict[NEGATIVE_IOU_KEY]
this_file_name = '{0:s}/positive_comparison.jpg'.format(output_dir_name)
_plot_comparison(
predictor_matrix=predictor_matrix,
model_metadata_dict=model_metadata_dict,
machine_mask_matrix_3d=machine_positive_mask_matrix_3d,
human_mask_matrix_3d=human_positive_mask_matrix_3d,
iou_by_channel=positive_iou_by_channel,
positive_flag=True, output_file_name=this_file_name)
if human_negative_mask_matrix_3d is None:
return
this_file_name = '{0:s}/negative_comparison.jpg'.format(output_dir_name)
_plot_comparison(
predictor_matrix=predictor_matrix,
model_metadata_dict=model_metadata_dict,
machine_mask_matrix_3d=machine_negative_mask_matrix_3d,
human_mask_matrix_3d=human_negative_mask_matrix_3d,
iou_by_channel=negative_iou_by_channel,
positive_flag=False, output_file_name=this_file_name)
def _run(input_file_name, cam_colour_map_name, max_colour_prctile_for_cam,
top_output_dir_name):
"""Plots Grad-CAM output (class-activation maps).
This is effectively the main method.
:param input_file_name: See documentation at top of file.
:param cam_colour_map_name: Same.
:param max_colour_prctile_for_cam: Same.
:param top_output_dir_name: Same.
:raises: TypeError: if input file contains class-activation maps for
soundings.
"""
main_gradcam_dir_name = '{0:s}/main_gradcam'.format(top_output_dir_name)
guided_gradcam_dir_name = '{0:s}/guided_gradcam'.format(top_output_dir_name)
file_system_utils.mkdir_recursive_if_necessary(
directory_name=main_gradcam_dir_name)
file_system_utils.mkdir_recursive_if_necessary(
directory_name=guided_gradcam_dir_name)
# Check input args.
error_checking.assert_is_geq(max_colour_prctile_for_cam, 0.)
error_checking.assert_is_leq(max_colour_prctile_for_cam, 100.)
cam_colour_map_object = pyplot.cm.get_cmap(cam_colour_map_name)
print 'Reading data from: "{0:s}"...'.format(input_file_name)
try:
gradcam_dict = gradcam.read_standard_file(input_file_name)
list_of_input_matrices = gradcam_dict.pop(gradcam.INPUT_MATRICES_KEY)
class_activation_matrix = gradcam_dict.pop(
gradcam.CLASS_ACTIVATIONS_KEY)
ggradcam_output_matrix = gradcam_dict.pop(gradcam.GUIDED_GRADCAM_KEY)
gradcam_metadata_dict = gradcam_dict
storm_ids = gradcam_metadata_dict[gradcam.STORM_IDS_KEY]
storm_times_unix_sec = gradcam_metadata_dict[gradcam.STORM_TIMES_KEY]
except ValueError:
gradcam_dict = gradcam.read_pmm_file(input_file_name)
list_of_input_matrices = gradcam_dict[gradcam.MEAN_INPUT_MATRICES_KEY]
class_activation_matrix = gradcam_dict[
gradcam.MEAN_CLASS_ACTIVATIONS_KEY]
ggradcam_output_matrix = gradcam_dict[gradcam.MEAN_GUIDED_GRADCAM_KEY]
for i in range(len(list_of_input_matrices)):
list_of_input_matrices[i] = numpy.expand_dims(
list_of_input_matrices[i], axis=0)
class_activation_matrix = numpy.expand_dims(
class_activation_matrix, axis=0)
ggradcam_output_matrix = numpy.expand_dims(
ggradcam_output_matrix, axis=0)
orig_gradcam_file_name = gradcam_dict[gradcam.STANDARD_FILE_NAME_KEY]
print 'Reading metadata from: "{0:s}"...'.format(orig_gradcam_file_name)
orig_gradcam_dict = gradcam.read_standard_file(orig_gradcam_file_name)
orig_gradcam_dict.pop(gradcam.INPUT_MATRICES_KEY)
orig_gradcam_dict.pop(gradcam.CLASS_ACTIVATIONS_KEY)
orig_gradcam_dict.pop(gradcam.GUIDED_GRADCAM_KEY)
gradcam_metadata_dict = orig_gradcam_dict
storm_ids = None
storm_times_unix_sec = None
num_spatial_dimensions = len(class_activation_matrix.shape) - 1
if num_spatial_dimensions == 1:
raise TypeError('This script is not yet equipped to plot '
'class-activation maps for soundings.')
# Read metadata for CNN.
model_file_name = gradcam_metadata_dict[gradcam.MODEL_FILE_NAME_KEY]
model_metafile_name = '{0:s}/model_metadata.p'.format(
os.path.split(model_file_name)[0]
)
print 'Reading model metadata from: "{0:s}"...'.format(model_metafile_name)
model_metadata_dict = cnn.read_model_metadata(model_metafile_name)
print SEPARATOR_STRING
# Do plotting.
if num_spatial_dimensions == 3:
_plot_3d_radar_cams(
radar_matrix=list_of_input_matrices[0],
class_activation_matrix=class_activation_matrix,
model_metadata_dict=model_metadata_dict,
cam_colour_map_object=cam_colour_map_object,
max_colour_prctile_for_cam=max_colour_prctile_for_cam,
output_dir_name=main_gradcam_dir_name,
storm_ids=storm_ids, storm_times_unix_sec=storm_times_unix_sec)
print SEPARATOR_STRING
_plot_3d_radar_cams(
radar_matrix=list_of_input_matrices[0],
ggradcam_output_matrix=ggradcam_output_matrix,
model_metadata_dict=model_metadata_dict,
cam_colour_map_object=cam_colour_map_object,
max_colour_prctile_for_cam=max_colour_prctile_for_cam,
output_dir_name=guided_gradcam_dir_name,
storm_ids=storm_ids, storm_times_unix_sec=storm_times_unix_sec)
else:
if len(list_of_input_matrices) == 3:
radar_matrix = list_of_input_matrices[1]
else:
radar_matrix = list_of_input_matrices[0]
_plot_2d_radar_cams(
radar_matrix=radar_matrix,
class_activation_matrix=class_activation_matrix,
model_metadata_dict=model_metadata_dict,
cam_colour_map_object=cam_colour_map_object,
max_colour_prctile_for_cam=max_colour_prctile_for_cam,
output_dir_name=main_gradcam_dir_name,
storm_ids=storm_ids, storm_times_unix_sec=storm_times_unix_sec)
print SEPARATOR_STRING
_plot_2d_radar_cams(
radar_matrix=radar_matrix,
ggradcam_output_matrix=ggradcam_output_matrix,
model_metadata_dict=model_metadata_dict,
cam_colour_map_object=cam_colour_map_object,
max_colour_prctile_for_cam=max_colour_prctile_for_cam,
output_dir_name=guided_gradcam_dir_name,
storm_ids=storm_ids, storm_times_unix_sec=storm_times_unix_sec)
def _run(input_gradcam_file_name, input_human_file_name,
output_gradcam_file_name):
"""Runs human novelty detection on class-activation maps.
This is effectively the main method.
:param input_gradcam_file_name: See documentation at top of file.
:param input_human_file_name: Same.
:param output_gradcam_file_name: Same.
:raises: TypeError: if `input_gradcam_file_name` was created by a net that
does both 2-D and 3-D convolution.
:raises: TypeError: if class-activation maps are not 2-D.
"""
print('Reading data from: "{0:s}"...'.format(input_human_file_name))
human_point_dict = human_polygons.read_points(input_human_file_name)
# TODO(thunderhoser): Deal with no human points.
human_grid_rows = human_point_dict[human_polygons.GRID_ROW_BY_POINT_KEY]
human_grid_columns = human_point_dict[
human_polygons.GRID_COLUMN_BY_POINT_KEY]
human_panel_rows = human_point_dict[human_polygons.PANEL_ROW_BY_POINT_KEY]
human_panel_columns = human_point_dict[
human_polygons.PANEL_COLUMN_BY_POINT_KEY]
full_storm_id_string = human_point_dict[human_polygons.STORM_ID_KEY]
storm_time_unix_sec = human_point_dict[human_polygons.STORM_TIME_KEY]
pmm_flag = full_storm_id_string is None and storm_time_unix_sec is None
print('Reading data from: "{0:s}"...'.format(input_gradcam_file_name))
if pmm_flag:
gradcam_dict = gradcam.read_pmm_file(input_gradcam_file_name)
else:
gradcam_dict = gradcam.read_standard_file(input_gradcam_file_name)
machine_region_dict = gradcam_dict[gradcam.REGION_DICT_KEY]
list_of_mask_matrices = machine_region_dict[gradcam.MASK_MATRICES_KEY]
if len(list_of_mask_matrices) == 3:
raise TypeError('This script cannot handle nets that do both 2-D and '
'3-D convolution.')
machine_mask_matrix = list_of_mask_matrices[0]
if pmm_flag:
storm_object_index = -1
else:
storm_object_index = tracking_utils.find_storm_objects(
all_id_strings=gradcam_dict[gradcam.FULL_IDS_KEY],
all_times_unix_sec=gradcam_dict[gradcam.STORM_TIMES_KEY],
id_strings_to_keep=[full_storm_id_string],
times_to_keep_unix_sec=numpy.array([storm_time_unix_sec],
dtype=int),
allow_missing=False)[0]
machine_mask_matrix = machine_mask_matrix[storm_object_index, ...]
num_spatial_dimensions = len(machine_mask_matrix.shape) - 1
if num_spatial_dimensions != 2:
raise TypeError(
'This script can compare only with 2-D class-activation'
' maps.')
if pmm_flag:
machine_polygon_objects = machine_region_dict[
gradcam.POLYGON_OBJECTS_KEY][0][0]
else:
machine_polygon_objects = machine_region_dict[
gradcam.POLYGON_OBJECTS_KEY][storm_object_index][0]