ROICaT
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API Documentation
ROICaT
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
_
_assert_mode (roicat.helpers.Equivalence_checker attribute)
_kwargs_allclose (roicat.helpers.Equivalence_checker attribute)
_system_info (roicat.util.ROICaT_Module attribute)
A
add_text_to_images() (in module roicat.helpers)
Aligner (class in roicat.tracking.alignment)
apply_warp_transform() (in module roicat.helpers)
attach_fully_connected_node() (in module roicat.tracking.clustering)
augment_FOV_images() (roicat.tracking.alignment.Aligner class method)
Auto_LogisticRegression (class in roicat.classification.classifier)
Autotuner_regression (class in roicat.classification.classifier)
B
best (roicat.helpers.Convergence_checker_optuna attribute)
bests (roicat.helpers.Convergence_checker_optuna attribute)
blur_ROIs() (roicat.tracking.blurring.ROI_Blurrer method)
bounded_logspace() (in module roicat.helpers)
C
catch_convergence_warnings (roicat.classification.classifier.Autotuner_regression attribute)
ccs (roicat.tracking.alignment.PhaseCorrelationRegistration attribute)
check() (roicat.helpers.Convergence_checker_optuna method)
check_completeness() (roicat.data_importing.Data_roicat method)
check_dataStructure__list_ofListOrArray_ofDtype() (in module roicat.util)
check_keys_subset() (in module roicat.helpers)
clahe() (in module roicat.tracking.alignment)
class_labels_index (roicat.data_importing.Data_roicat attribute)
class_labels_raw (roicat.data_importing.Data_roicat attribute)
classify() (roicat.helpers.ImageLabeler method)
cluster_quality_metrics() (in module roicat.tracking.clustering)
Clusterer (class in roicat.tracking.clustering)
compare_file_hashes() (in module roicat.helpers)
compose_remappingIdx() (in module roicat.helpers)
compose_transform_matrices() (in module roicat.helpers)
compute_cluster_similarity_matrices() (in module roicat.helpers)
compute_colored_FOV() (in module roicat.visualization)
compute_quality_metrics() (roicat.tracking.clustering.Clusterer method)
compute_similarity_blockwise() (roicat.tracking.similarity_graph.ROI_graph method)
confusion_matrix() (in module roicat.helpers)
Convergence_checker_optuna (class in roicat.helpers)
convert_phaseCorrelationImage_to_shifts() (in module roicat.tracking.alignment)
convolve() (roicat.helpers.Convolver_1d method)
Convolver_1d (class in roicat.helpers)
cosine_kernel_2D() (in module roicat.helpers)
cosine_similarity_customIdx() (in module roicat.tracking.similarity_graph)
crop_cluster_ims() (in module roicat.visualization)
cv (roicat.classification.classifier.Autotuner_regression attribute)
cv2RemappingIdx_to_pytorchFlowField() (in module roicat.helpers)
D
Data_caiman (class in roicat.data_importing)
Data_roicat (class in roicat.data_importing)
Data_roiextractors (class in roicat.data_importing)
Data_suite2p (class in roicat.data_importing)
Dataloader_ROInet (class in roicat.ROInet)
dataset_simCLR (class in roicat.ROInet)
deep_update_dict() (in module roicat.helpers)
discard_UCIDs_with_fewer_matches() (in module roicat.util)
display_cropped_cluster_ims() (in module roicat.visualization)
display_labeled_ROIs() (in module roicat.visualization)
display_toggle_image_stack() (in module roicat.visualization)
download_file() (in module roicat.helpers)
dtype (roicat.helpers.Convolver_1d attribute)
(roicat.helpers.Toeplitz_convolution2d attribute)
E
end_session() (roicat.helpers.ImageLabeler method)
Equivalence_checker (class in roicat.helpers)
evaluate_model() (roicat.classification.classifier.Auto_LogisticRegression method)
export_svg_hv_bokeh() (in module roicat.helpers)
extract_zip() (in module roicat.helpers)
F
fill_in_dict() (in module roicat.helpers)
find_geometric_transformation() (in module roicat.helpers)
find_nonredundant_idx() (in module roicat.helpers)
find_optimal_parameters_for_pruning() (roicat.tracking.clustering.Clusterer method)
find_paths() (in module roicat.helpers)
fit() (roicat.classification.classifier.Autotuner_regression method)
(roicat.tracking.clustering.Clusterer method)
fit_geometric() (roicat.tracking.alignment.Aligner method)
fit_nonrigid() (roicat.tracking.alignment.Aligner method)
fit_sequentialHungarian() (roicat.tracking.clustering.Clusterer method)
fix_paths() (in module roicat.data_importing)
flatten_dict() (in module roicat.helpers)
flowField_to_remappingIdx() (in module roicat.helpers)
fn_loss (roicat.classification.classifier.Autotuner_regression attribute)
forward() (roicat.ROInet.ScaleDynamicRange method)
(roicat.ROInet.TileChannels method)
(roicat.ROInet.Unsqueeze method)
FOV_height (roicat.data_importing.Data_roicat attribute)
FOV_images (roicat.data_importing.Data_roicat attribute)
FOV_width (roicat.data_importing.Data_roicat attribute)
frame_shape (roicat.tracking.blurring.ROI_Blurrer attribute)
G
generalised_logistic_function() (in module roicat.helpers)
generate_dataloader() (roicat.ROInet.ROInet_embedder method)
(roicat.ROInet.ROInet_embedder_original method)
generate_latents() (roicat.ROInet.ROInet_embedder method)
(roicat.ROInet.ROInet_embedder_original method)
get_balanced_class_weights() (in module roicat.helpers)
get_balanced_sample_weights() (in module roicat.helpers)
get_default_parameters() (in module roicat.util)
get_dir_contents() (in module roicat.helpers)
get_flowFields() (roicat.tracking.alignment.Aligner method)
get_idx_in_kRange() (in module roicat.tracking.similarity_graph)
get_labels() (roicat.helpers.ImageLabeler method)
get_maxIntensityProjection_spatialFootprints() (roicat.data_importing.Data_roicat method)
get_nd_butterworth_filter() (in module roicat.helpers)
get_nums_from_string() (in module roicat.helpers)
get_roicat_version() (in module roicat.util)
get_ROIsAligned_maxIntensityProjection() (roicat.tracking.alignment.Aligner method)
get_ROIsBlurred_maxIntensityProjection() (roicat.tracking.blurring.ROI_Blurrer method)
get_spread_out_points() (in module roicat.visualization)
grayscale_to_rgb() (in module roicat.helpers)
H
h5_load() (in module roicat.helpers)
hash_file() (in module roicat.helpers)
I
idx2bool() (in module roicat.helpers)
idx_to_oneHot() (in module roicat.helpers)
image_array (roicat.helpers.ImageLabeler attribute)
ImageLabeler (class in roicat.helpers)
import_cnn_caiman_preds() (roicat.data_importing.Data_caiman method)
import_FOV_images() (roicat.data_importing.Data_caiman method)
(roicat.data_importing.Data_suite2p method)
import_from_dict() (roicat.data_importing.Data_roicat method)
import_neuropil_masks() (roicat.data_importing.Data_suite2p method)
import_overall_caiman_labels() (roicat.data_importing.Data_caiman method)
import_ROI_centeredImages() (roicat.data_importing.Data_caiman method)
import_spatialFootprints() (roicat.data_importing.Data_caiman method)
(roicat.data_importing.Data_suite2p method)
ims_moving_filt (roicat.tracking.alignment.PhaseCorrelationRegistration attribute)
ims_registered (roicat.tracking.alignment.PhaseCorrelationRegistration attribute)
ims_template_filt (roicat.tracking.alignment.PhaseCorrelationRegistration attribute)
index (roicat.helpers.ParallelExecutionError attribute)
index_with_nans() (in module roicat.helpers)
invert_remappingIdx() (in module roicat.helpers)
invert_warp_matrix() (in module roicat.helpers)
J
json_load() (in module roicat.helpers)
json_save() (in module roicat.helpers)
K
k (roicat.helpers.Toeplitz_convolution2d attribute)
kernel (roicat.helpers.Convolver_1d attribute)
kernel_halfWidth (roicat.tracking.blurring.ROI_Blurrer attribute)
key_end (roicat.helpers.ImageLabeler attribute)
key_next (roicat.helpers.ImageLabeler attribute)
key_prev (roicat.helpers.ImageLabeler attribute)
kwargs_convergence (roicat.classification.classifier.Autotuner_regression attribute)
L
labels_ (roicat.helpers.ImageLabeler attribute)
labels_to_labelsBySession() (in module roicat.util)
lazy_repeat_obj (class in roicat.helpers)
length (roicat.helpers.scipy_sparse_csr_with_length attribute)
load() (roicat.util.ROICaT_Module method)
Load_ONNX_model_sklearnLogisticRegression (class in roicat.classification.classifier)
LossFunction_CrossEntropy_CV (class in roicat.classification.classifier)
M
make_batches() (in module roicat.helpers)
make_conjunctive_distance_matrix() (roicat.tracking.clustering.Clusterer class method)
make_Fourier_mask() (in module roicat.helpers)
make_label_variants() (in module roicat.tracking.clustering)
make_normalized_similarities() (roicat.tracking.similarity_graph.ROI_graph method)
make_pruned_similarity_graphs() (roicat.tracking.clustering.Clusterer method)
make_session_bool() (in module roicat.util)
make_smaller_data() (in module roicat.data_importing)
make_spectral_mask() (in module roicat.tracking.alignment)
map_parallel() (in module roicat.helpers)
mask (roicat.tracking.alignment.PhaseCorrelationRegistration attribute)
mask_image_border() (in module roicat.helpers)
mask_UCIDs_by_label() (in module roicat.util)
mask_UCIDs_with_iscell() (in module roicat.util)
match_arrays_with_ucids() (in module roicat.util)
match_arrays_with_ucids_inverse() (in module roicat.util)
matlab_load() (in module roicat.helpers)
matlab_save() (in module roicat.helpers)
merge_dicts() (in module roicat.helpers)
merge_sparse_arrays() (in module roicat.helpers)
mode (roicat.helpers.Toeplitz_convolution2d attribute)
model_class (roicat.classification.classifier.Autotuner_regression attribute)
module
roicat.classification
roicat.classification.classifier
roicat.data_importing
roicat.helpers
roicat.pipelines
roicat.ROInet
roicat.tracking
roicat.tracking.alignment
roicat.tracking.blurring
roicat.tracking.clustering
roicat.tracking.scatteringWaveletTransformer
roicat.tracking.similarity_graph
roicat.util
roicat.visualization
N
n_jobs_optuna (roicat.classification.classifier.Autotuner_regression attribute)
n_roi (roicat.data_importing.Data_roicat attribute)
n_roi_total (roicat.data_importing.Data_roicat attribute)
n_sessions (roicat.data_importing.Data_roicat attribute)
n_startup (roicat.classification.classifier.Autotuner_regression attribute)
next_img() (roicat.helpers.ImageLabeler method)
normalize_images (roicat.helpers.ImageLabeler attribute)
O
original_exception (roicat.helpers.ParallelExecutionError attribute)
P
pad_mode (roicat.helpers.Convolver_1d attribute)
ParallelExecutionError
params (roicat.classification.classifier.Autotuner_regression attribute)
path_csv (roicat.helpers.ImageLabeler attribute)
phase_correlation() (in module roicat.tracking.alignment)
PhaseCorrelationRegistration (class in roicat.tracking.alignment)
pickle_load() (in module roicat.helpers)
pickle_save() (in module roicat.helpers)
pipeline_tracking() (in module roicat.pipelines)
plot_C_curve() (roicat.classification.classifier.Auto_LogisticRegression method)
plot_confusion_matrix() (in module roicat.visualization)
plot_distSame() (roicat.tracking.clustering.Clusterer method)
plot_image_grid() (in module roicat.helpers)
plot_kernel (roicat.tracking.blurring.ROI_Blurrer attribute)
plot_resized_comparison() (roicat.ROInet.Resizer_ROI_images method)
plot_similarity_relationships() (roicat.tracking.clustering.Clusterer method)
prepare_directory_for_loading() (in module roicat.helpers)
prepare_directory_for_saving() (in module roicat.helpers)
prepare_filepath_for_loading() (in module roicat.helpers)
prepare_filepath_for_saving() (in module roicat.helpers)
prepare_params() (in module roicat.helpers)
prepare_path() (in module roicat.helpers)
prev_img() (roicat.helpers.ImageLabeler method)
pydata_sparse_to_torch_coo() (in module roicat.helpers)
R
rand_cmap() (in module roicat.helpers)
register() (roicat.tracking.alignment.PhaseCorrelationRegistration method)
remap_images() (in module roicat.helpers)
remap_sparse_images() (in module roicat.helpers)
remappingIdx_to_flowField() (in module roicat.helpers)
remove_redundant_elements() (in module roicat.helpers)
resize_affine() (in module roicat.ROInet)
resize_factor (roicat.helpers.ImageLabeler attribute)
resize_images() (in module roicat.helpers)
resize_ROIs() (roicat.ROInet.Resizer_ROI_images class method)
(roicat.ROInet.ROInet_embedder_original class method)
Resizer_ROI_images (class in roicat.ROInet)
ROI_Blurrer (class in roicat.tracking.blurring)
ROI_graph (class in roicat.tracking.similarity_graph)
ROI_images (roicat.data_importing.Data_roicat attribute)
roicat.classification
module
roicat.classification.classifier
module
roicat.data_importing
module
roicat.helpers
module
roicat.pipelines
module
roicat.ROInet
module
roicat.tracking
module
roicat.tracking.alignment
module
roicat.tracking.blurring
module
roicat.tracking.clustering
module
roicat.tracking.scatteringWaveletTransformer
module
roicat.tracking.similarity_graph
module
roicat.util
module
roicat.visualization
module
ROICaT_Module (class in roicat.util)
ROInet_embedder (class in roicat.ROInet)
ROInet_embedder_original (class in roicat.ROInet)
run() (roicat.helpers.ImageLabeler method)
S
s_NN (roicat.tracking.similarity_graph.ROI_graph attribute)
s_NN_z (roicat.tracking.clustering.Clusterer attribute)
(roicat.tracking.similarity_graph.ROI_graph attribute)
s_sesh (roicat.tracking.clustering.Clusterer attribute)
(roicat.tracking.similarity_graph.ROI_graph attribute)
s_sesh_inv (roicat.tracking.clustering.Clusterer attribute)
s_sf (roicat.tracking.clustering.Clusterer attribute)
(roicat.tracking.similarity_graph.ROI_graph attribute)
s_SWT (roicat.tracking.similarity_graph.ROI_graph attribute)
s_SWT_z (roicat.tracking.clustering.Clusterer attribute)
(roicat.tracking.similarity_graph.ROI_graph attribute)
sample_weight (roicat.classification.classifier.Autotuner_regression attribute)
save() (roicat.util.ROICaT_Module method)
save_classification() (roicat.helpers.ImageLabeler method)
save_csv (roicat.helpers.ImageLabeler attribute)
save_gif() (in module roicat.helpers)
save_model() (roicat.classification.classifier.Autotuner_regression method)
ScaleDynamicRange (class in roicat.ROInet)
scipy_sparse_csr_with_length (class in roicat.helpers)
scipy_sparse_to_torch_coo() (in module roicat.helpers)
score_labels() (in module roicat.tracking.clustering)
select_region_scatterPlot() (in module roicat.visualization)
serializable_dict (roicat.util.ROICaT_Module property)
session_bool (roicat.data_importing.Data_roicat attribute)
set_caimanLabels() (roicat.data_importing.Data_caiman method)
set_caimanPreds() (roicat.data_importing.Data_caiman method)
set_class_labels() (roicat.data_importing.Data_roicat method)
set_device() (in module roicat.helpers)
set_FOV_images() (roicat.data_importing.Data_roicat method)
set_FOVHeightWidth() (roicat.data_importing.Data_roicat method)
set_ROI_images() (roicat.data_importing.Data_roicat method)
set_spatialFootprints() (roicat.data_importing.Data_roicat method)
set_spectral_mask() (roicat.tracking.alignment.PhaseCorrelationRegistration method)
shift_along_axis() (in module roicat.tracking.alignment)
shifts (roicat.tracking.alignment.PhaseCorrelationRegistration attribute)
show_item_tree() (in module roicat.helpers)
simple_cmap() (in module roicat.helpers)
sparse_mask() (in module roicat.helpers)
sparse_to_dense_fill() (in module roicat.helpers)
spatialFootprints (roicat.data_importing.Data_roicat attribute)
squeeze_integers() (in module roicat.helpers)
squeeze_UCID_labels() (in module roicat.util)
start_index (roicat.helpers.ImageLabeler attribute)
SWT (class in roicat.tracking.scatteringWaveletTransformer)
system_info() (in module roicat.util)
T
tile_channels() (roicat.ROInet.dataset_simCLR method)
TileChannels (class in roicat.ROInet)
Toeplitz_convolution2d (class in roicat.helpers)
torch_pca() (in module roicat.helpers)
trace_correction (roicat.helpers.Convolver_1d attribute)
transform() (roicat.tracking.scatteringWaveletTransformer.SWT method)
transform_images() (roicat.tracking.alignment.Aligner method)
transform_images_geometric() (roicat.tracking.alignment.Aligner method)
transform_images_nonrigid() (roicat.tracking.alignment.Aligner method)
transform_ROIs() (roicat.tracking.alignment.Aligner method)
type (roicat.data_importing.Data_roicat attribute)
U
um_per_pixel (roicat.data_importing.Data_roicat attribute)
Unsqueeze (class in roicat.ROInet)
V
verbose (roicat.classification.classifier.Autotuner_regression attribute)
(roicat.helpers.ImageLabeler attribute)
(roicat.tracking.blurring.ROI_Blurrer attribute)
(roicat.tracking.clustering.Clusterer attribute)
visualize_blocks() (roicat.tracking.similarity_graph.ROI_graph method)
W
warp_matrix_to_remappingIdx() (in module roicat.helpers)
X
X (roicat.classification.classifier.Autotuner_regression attribute)
x_shape (roicat.helpers.Toeplitz_convolution2d attribute)
Y
y (roicat.classification.classifier.Autotuner_regression attribute)
yaml_load() (in module roicat.helpers)
yaml_save() (in module roicat.helpers)
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