From 07029893266dad1868a975bc27c22be06cf08bf1 Mon Sep 17 00:00:00 2001 From: Timon Stegmaier Date: Tue, 12 Nov 2024 15:33:12 +0100 Subject: [PATCH 1/2] fix: typo --- cellacdc/myutils.py | 6 +++--- .../CellACDC_normal_division_tracker.py | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cellacdc/myutils.py b/cellacdc/myutils.py index e527bc51..01938dfb 100644 --- a/cellacdc/myutils.py +++ b/cellacdc/myutils.py @@ -3325,7 +3325,7 @@ def _download_cellpose_germlineNuclei_model(): def _download_omnipose_models(): urls, file_sizes = _model_url('omnipose') temp_model_path = tempfile.mkdtemp() - final_model_path = os.path.expanduser('~\.cellpose\models') + final_model_path = os.path.expanduser(r'~\.cellpose\models') for url, file_size in zip(urls, file_sizes): filename = url.split('/')[-1] final_dst = os.path.join(final_model_path, filename) @@ -3501,7 +3501,7 @@ def are_acdc_dfs_equal(df_left, df_right): def is_pos_folderpath(folderpath): foldername = os.path.basename(folderpath) is_valid_pos_folder = ( - re.search('^Position_(\d+)$', foldername) is not None + re.search(r'^Position_(\d+)$', foldername) is not None and os.path.isdir(folderpath) and os.path.exists(os.path.join(folderpath, 'Images')) ) @@ -3585,7 +3585,7 @@ def validate_images_path(input_path: os.PathLike, create_dirs_tree=False): parent_dir = os.path.dirname(input_path) parent_foldername = os.path.basename(parent_dir) is_pos_folder = ( - re.search('^Position_(\d+)$', parent_foldername) is not None + re.search(r'^Position_(\d+)$', parent_foldername) is not None and os.path.isdir(parent_dir) ) if not is_pos_folder: diff --git a/cellacdc/trackers/CellACDC_normal_division/CellACDC_normal_division_tracker.py b/cellacdc/trackers/CellACDC_normal_division/CellACDC_normal_division_tracker.py index 581b186f..328cc297 100644 --- a/cellacdc/trackers/CellACDC_normal_division/CellACDC_normal_division_tracker.py +++ b/cellacdc/trackers/CellACDC_normal_division/CellACDC_normal_division_tracker.py @@ -69,7 +69,7 @@ def reorg_sister_cells_inner_func(row): return values -def reorg_sister_cells_for_inport(df): +def reorg_sister_cells_for_import(df): """ Reorganizes the sister cells for import. @@ -987,7 +987,7 @@ def insert_lineage_df(self, lineage_df, frame_i, propagate_back=False, propagate elif quick and (propagate_back or propagate_fwd or update_fams or consider_children): raise ValueError('Quick is True, other options are not supported.') - lineage_df = reorg_sister_cells_for_inport(lineage_df) + lineage_df = reorg_sister_cells_for_import(lineage_df) lineage_df = filter_cols(lineage_df) if frame_i == len(self.lineage_list): if not quick: @@ -1104,7 +1104,7 @@ def load_lineage_df_list(self, df_li): ) df = filter_cols(df) - df = reorg_sister_cells_for_inport(df) + df = reorg_sister_cells_for_import(df) self.frames_for_dfs.add(i) df_li_new.append(df) From 92bc5401330389ce9b1305c805292bfaaa95a37f Mon Sep 17 00:00:00 2001 From: Timon Stegmaier Date: Tue, 12 Nov 2024 19:31:49 +0100 Subject: [PATCH 2/2] fix: small inconstancy errors in Normal division: lineage tree --- cellacdc/_debug.py | 2 +- .../CellACDC_normal_division_tracker.py | 13 +++++++++---- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/cellacdc/_debug.py b/cellacdc/_debug.py index 0c50232d..c0c4bd2c 100644 --- a/cellacdc/_debug.py +++ b/cellacdc/_debug.py @@ -87,4 +87,4 @@ def _debug_lineage_tree(guiWin): else: pgshow(acdc_df) - printl(posData.tracked_lost_centroids) \ No newline at end of file + # printl(posData.tracked_lost_centroids) \ No newline at end of file diff --git a/cellacdc/trackers/CellACDC_normal_division/CellACDC_normal_division_tracker.py b/cellacdc/trackers/CellACDC_normal_division/CellACDC_normal_division_tracker.py index 328cc297..9eb14959 100644 --- a/cellacdc/trackers/CellACDC_normal_division/CellACDC_normal_division_tracker.py +++ b/cellacdc/trackers/CellACDC_normal_division/CellACDC_normal_division_tracker.py @@ -21,7 +21,7 @@ def filter_cols(df): Returns: - pandas.DataFrame: The filtered DataFrame containing only the specified columns. """ - lin_tree_cols = {'generation_num_tree', 'root_ID_tree', 'sister_ID_tree', 'parent_ID_tree', 'parent_ID_tree', 'emerg_frame_i', 'division_frame_i'} + lin_tree_cols = {'generation_num_tree', 'root_ID_tree', 'sister_ID_tree', 'parent_ID_tree', 'parent_ID_tree', 'emerg_frame_i', 'division_frame_i', 'is_history_known'} sis_cols = {col for col in df.columns if col.startswith('sister_ID_tree')} lin_tree_cols = lin_tree_cols | sis_cols return df[list(lin_tree_cols)] @@ -174,6 +174,7 @@ def added_lineage_tree_to_cca_df(added_lineage_tree): - 'parent_ID_tree' - 'root_ID_tree' - 'sister_ID_tree' + - 'is_history_known' """ cca_df = pd.DataFrame() @@ -184,6 +185,9 @@ def added_lineage_tree_to_cca_df(added_lineage_tree): cca_df['parent_ID_tree'] = [row[2] for row in added_lineage_tree] cca_df['root_ID_tree'] = [row[4] for row in added_lineage_tree] cca_df['sister_ID_tree'] = [row[5] for row in added_lineage_tree] + cca_df['is_history_known'] = cca_df['parent_ID_tree'] != -1 + cca_df['is_history_known'] = cca_df['is_history_known'].astype(int) + cca_df = cca_df.set_index('Cell_ID') return cca_df @@ -736,11 +740,10 @@ def create_tracked_frame(self, frame_i, mother_daughters, IDs_prev, IDs_curr_unt for ID in new_unknown_IDs: # print(f'Frame {frame_i}: New cell ID {ID} suspected of being a cell from the outside.') self.families.append([(ID, 1)]) - added_lineage_tree.append((-1, ID, -1, 1, ID, [-1] * (self.max_daughter-1))) + added_lineage_tree.append((frame_i, ID, -1, 1, ID, [-1] * (self.max_daughter-1))) for mother, _ in mother_daughters: - mother_ID = IDs_prev[mother] daughter_IDs = daughter_dict[mother] found = False # flag to track if a family was associated @@ -894,9 +897,11 @@ def update_gen_df_from_df(self, df, frame_i): Cell_info['generation_num_tree'] = 1 Cell_info['root_ID_tree'] = Cell_info['Cell_ID'] Cell_info['sister_ID_tree'] = [-1] + Cell_info['is_history_known'] = False corrected_df = pd.concat([corrected_df, Cell_info.to_frame().T]) continue + Cell_info['is_history_known'] = True parent_cell = unique_Cell_ID_df.loc[Cell_info['parent_ID_tree']] Cell_info['generation_num_tree'] = parent_cell['generation_num_tree'] + 1 Cell_info['root_ID_tree'] = parent_cell['root_ID_tree'] @@ -1056,7 +1061,7 @@ def insert_lineage_df(self, lineage_df, frame_i, propagate_back=False, propagate def propagate(self, frame_i, Cell_IDs_fixed=None): """ Propagates the changes made to self.lineage_list at frame frame_i to the general DataFrame (self.general_df), families (self.families), and lineage list (self.gen_df_to_df_li()). The propagation can be done in both directions, and fixed cell IDs can be provided (in this case only those are propegated and the other Cell_IDs in the specified frame are ignored.) - + Also updates is_history_known Parameters: - frame_i (int): The index of the frame to be propagated. - Cell_IDs_fixed (list, optional): List of fixed cell IDs. Defaults to None.