************** CELLFINDER LOG ************** Analysis carried out: 2020-06-17_14-45-45 Output directory: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test Current directory: C:\Users\guill Version: 0.3.14 ************** GIT INFO ************** Gitpython is not installed. Cannot check if software is in a git repository ************** COMMAND LINE ARGUMENTS ************** Command: C:\Users\guill\miniconda3\envs\cellfinder\Scripts\cellfinder Input arguments: ['-s', 'D:\\DATA STAGE\\190514_P7_CFOS_ES2_RIGHT\\C01', '-b', 'D:\\DATA STAGE\\190514_P7_CFOS_ES2_RIGHT\\C00', '-o', 'D:\\DATA STAGE\\190514_P7_CFOS_ES2_RIGHT\\test', '-x', '4.7944', '-y', '4.7944', '-z', '5', '--max-ram', '8', '--summarise'] ************** VARIABLES ************** Namespace: signal_planes_paths: ['D:\\DATA STAGE\\190514_P7_CFOS_ES2_RIGHT\\C01'] background_planes_path: ['D:\\DATA STAGE\\190514_P7_CFOS_ES2_RIGHT\\C00'] output_dir: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test register: False summarise: True figures: False signal_ch_ids: None background_ch_id: None sort_input_file: False no_save_downsampled: False affine_n_steps: 6 affine_use_n_steps: 5 freeform_n_steps: 6 freeform_use_n_steps: 4 bending_energy_weight: 0.95 grid_spacing: -10 smoothing_sigma_reference: -1.0 smoothing_sigma_floating: -1.0 histogram_n_bins_floating: 128 histogram_n_bins_reference: 128 registration_config: c:\users\guill\miniconda3\envs\cellfinder\lib\site-packages\cellfinder\config\cellfinder.conf.custom x_pixel_um: 4.7944 y_pixel_um: 4.7944 z_pixel_um: 5.0 x_pixel_um_network: 1 y_pixel_um_network: 1 z_pixel_um_network: 5 orientation: coronal flip_x: False flip_y: False flip_z: False rotation: x0y0z0 no_detection: False no_classification: False no_standard_space: False start_plane: 0 end_plane: -1 save_planes: False outlier_keep: False artifact_keep: False max_cluster_size: 100000 soma_diameter: 16 ball_xy_size: 6 ball_z_size: 15 ball_overlap_fraction: 0.6 log_sigma_size: 0.2 n_sds_above_mean_thresh: 10 soma_spread_factor: 1.4 trained_model: None model_weights: None network_depth: 50 batch_size: 32 cube_width: 50 cube_height: 50 cube_depth: 20 save_empty_cubes: False atlas_config: None coordinates_order: [0, 1, 2] cells_only: True scale_cell_coordinates: True heatmap: True heatmap_binning: 100 heatmap_smooth: 100 mask_figures: True no_boundaries: False transform_all: False n_free_cpus: 2 max_ram: 8.0 save_csv: False debug: False metadata: None no_atlas: False atlas: allen_2017_10um no_models: False model: resnet50_tv install_path: C:\Users\guill\.cellfinder download_path: C:\Users\guill\AppData\Local\Temp\tmpjxgt1egg no_amend_config: False Paths: output_dir: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test registration_output_folder: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration downsampled_background: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\downsampled.nii tmp__downsampled_filtered: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\downsampled_filtered.nii registered_atlas_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\registered_atlas.nii hemispheres_atlas_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\registered_hemispheres.nii volume_csv_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\volumes.csv tmp__affine_registered_atlas_brain_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\affine_registered_atlas_brain.nii tmp__freeform_registered_atlas_brain_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\freeform_registered_atlas_brain.nii tmp__inverse_freeform_registered_atlas_brain_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\inverse_freeform_registered_brain.nii registered_atlas_img_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\registered_atlas.nii registered_hemispheres_img_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\registered_hemispheres.nii affine_matrix_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\affine_matrix.txt invert_affine_matrix_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\invert_affine_matrix.txt control_point_file_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\control_point_file.nii inverse_control_point_file_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\inverse_control_point_file.nii tmp__affine_log_file_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\affine.log tmp__affine_error_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\affine.err tmp__freeform_log_file_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\freeform.log tmp__freeform_error_file_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\freeform.err tmp__inverse_freeform_log_file_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\inverse_freeform.log tmp__inverse_freeform_error_file_path: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\inverse_freeform.err tmp__segmentation_log_file: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\segment.log tmp__segmentation_error_file: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\segment.err tmp__invert_affine_log_file: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\invert_affine.log tmp__invert_affine_error_file: D:\DATA STAGE\190514_P7_CFOS_ES2_RIGHT\test\registration\invert_affine.err ************** LOGGING ************** 2020-06-17 14:45:45 PM - INFO - MainProcess fancylog.py:265 - Starting logging 2020-06-17 14:45:45 PM - INFO - MainProcess fancylog.py:267 - Multiprocessing-logging module found. Logging from all processes 2020-06-17 14:45:45 PM - INFO - MainProcess main.py:32 - Registering to atlas 2020-06-17 14:45:45 PM - INFO - MainProcess prep.py:402 - Checking whether the atlas exists 2020-06-17 14:45:45 PM - INFO - MainProcess prep.py:433 - c:\users\guill\miniconda3\envs\cellfinder\lib\site-packages\cellfinder\config\cellfinder.conf.custom 2020-06-17 14:45:45 PM - DEBUG - MainProcess prep.py:414 - Making registration directory 2020-06-17 14:45:45 PM - DEBUG - MainProcess system.py:132 - Determining the maximum number of CPU cores to use 2020-06-17 14:45:45 PM - DEBUG - MainProcess system.py:141 - Number of CPU cores available is: 6 2020-06-17 14:45:45 PM - DEBUG - MainProcess system.py:166 - Setting number of processes to: 6 2020-06-17 14:45:45 PM - INFO - MainProcess run.py:35 - Downsampled data and reoriented atlas exists, skipping. 2020-06-17 14:45:45 PM - INFO - MainProcess main.py:168 - Image: channel_0 already downsampled, skipping. 2020-06-17 14:45:45 PM - INFO - MainProcess main.py:171 - Registering 2020-06-17 14:45:45 PM - INFO - MainProcess main.py:203 - Starting affine registration