From 9a02e4f4e03604be6a6480748eab768b6393fbc2 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Thu, 2 May 2019 14:38:45 +0200 Subject: [PATCH] fixed bug due to removing outlier detection --- mtor/workflows.py | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/mtor/workflows.py b/mtor/workflows.py index e600d20..a9694d0 100644 --- a/mtor/workflows.py +++ b/mtor/workflows.py @@ -12,8 +12,7 @@ from .dataproc import ( construct_data_frame, find_guard_threshold, check_guards, - find_outliers, - select_on_guards_and_outliers, + select_on_guards, smooth_rolling_min, smooth_savgol_filter, find_extremas, @@ -23,15 +22,14 @@ from .dataproc import ( from .postproc import ( stem_file_list, annotate_color_coded_images, - sort_cut_images, - remove_cuts_dir, + rename_cut_images, ) def prescan_workflow(folder, top, right, bottom, left, **kargs): print("1/5: scanning tifs for common autocontrast values") - parameters = Parameters(folder, top, right, bottom, left) + parameters = Parameters(folder, top, right, bottom, left, **kargs) parameters = scan_tifs(parameters) parameters.offset = parameters.intensity_min @@ -64,9 +62,8 @@ def data_workflow(stats_results, parameters): find_guard_threshold(data_frame, parameters) data_frame = check_guards(data_frame, parameters) - data_frame = find_outliers(data_frame, parameters) - selected_df = select_on_guards_and_outliers(data_frame, parameters) + selected_df = select_on_guards(data_frame, parameters) selected_df = smooth_rolling_min(selected_df, parameters) selected_df = smooth_savgol_filter(selected_df, parameters) @@ -79,10 +76,9 @@ def data_workflow(stats_results, parameters): def postprocessing_workflow(selected_files, parameters): - print("4/5: Post processing, sorting cut images") + print("4/5: Post processing, renaming cut images") file_stems = stem_file_list(selected_files) - sort_cut_images(file_stems, parameters) - remove_cuts_dir(parameters) + rename_cut_images(file_stems, parameters) print("5/5: Post processing, annotating color coded images") annotate_color_coded_images(file_stems, parameters) return WorkflowResult(None, parameters) @@ -96,9 +92,8 @@ def cached_data_workflow(folder): data_frame, parameters = load_temp(folder) find_guard_threshold(data_frame, parameters) data_frame = check_guards(data_frame, parameters) - data_frame = find_outliers(data_frame, parameters) - selected_df = select_on_guards_and_outliers(data_frame, parameters) + selected_df = select_on_guards(data_frame, parameters) selected_df = smooth_rolling_min(selected_df, parameters) selected_df = smooth_savgol_filter(selected_df, parameters)