spacr 0.5.0__py3-none-any.whl → 0.9.1__py3-none-any.whl

spacr/utils.py

@@ -10,7 +10,7 @@ import skimage.measure as measure
 from skimage.transform import resize as resizescikit
 from skimage.morphology import dilation, square
 from skimage.measure import find_contours
-from skimage.segmentation import clear_border
+from skimage.segmentation import clear_border, find_boundaries
 from scipy.stats import pearsonr
 
 from collections import defaultdict, OrderedDict
@@ -431,7 +431,7 @@ def close_multiprocessing_processes():
 
 def check_mask_folder(src,mask_fldr):
     
-    mask_folder = os.path.join(src,'norm_channel_stack',mask_fldr)
+    mask_folder = os.path.join(src,'masks',mask_fldr)
     stack_folder = os.path.join(src,'stack')
 
     if not os.path.exists(mask_folder):
@@ -1266,9 +1266,9 @@ def _pivot_counts_table(db_path):
     
 def _get_cellpose_channels(src, nucleus_channel, pathogen_channel, cell_channel):
 
-    cell_mask_path = os.path.join(src, 'norm_channel_stack', 'cell_mask_stack')
-    nucleus_mask_path = os.path.join(src, 'norm_channel_stack', 'nucleus_mask_stack')
-    pathogen_mask_path = os.path.join(src, 'norm_channel_stack', 'pathogen_mask_stack')
+    cell_mask_path = os.path.join(src, 'masks', 'cell_mask_stack')
+    nucleus_mask_path = os.path.join(src, 'masks', 'nucleus_mask_stack')
+    pathogen_mask_path = os.path.join(src, 'masks', 'pathogen_mask_stack')
 
 
     if os.path.exists(cell_mask_path) or os.path.exists(nucleus_mask_path) or os.path.exists(pathogen_mask_path):
@@ -3088,17 +3088,19 @@ def _object_filter(df, object_type, size_range, intensity_range, mask_chans, mas
     return df
 
 def _get_regex(metadata_type, img_format, custom_regex=None):
+    
+    print(f"Image_format: {img_format}")
 
     if img_format == None:
-        img_format == '.tif'
+        img_format == 'tif'
     if metadata_type == 'cellvoyager':
-        regex = f'(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*){img_format}'
+        regex = f"(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*).{img_format}"
     elif metadata_type == 'cq1':
-        regex = f'W(?P<wellID>.*)F(?P<fieldID>.*)T(?P<timeID>.*)Z(?P<sliceID>.*)C(?P<chanID>.*){img_format}'
+        regex = f"W(?P<wellID>.*)F(?P<fieldID>.*)T(?P<timeID>.*)Z(?P<sliceID>.*)C(?P<chanID>.*).{img_format}"
     elif metadata_type == 'auto':
-        regex = f'(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>.*)C(?P<chanID>.*).tif'     
+        regex = f"(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>.*)C(?P<chanID>.*).tif"     
     elif metadata_type == 'custom':
-        regex = f'({custom_regex}){img_format}'
+        regex = f"({custom_regex}){img_format}"
         
     print(f'regex mode:{metadata_type} regex:{regex}')
     return regex
@@ -4507,6 +4509,76 @@ def _merge_cells_based_on_parasite_overlap(parasite_mask, cell_mask, nuclei_mask
     relabeled_cell_mask, _ = label(cell_mask, return_num=True)
     return relabeled_cell_mask.astype(np.uint16)
 
+def _merge_cells_without_nucleus(adj_cell_mask: np.ndarray, nuclei_mask: np.ndarray):
+    """
+    Relabel any cell that lacks a nucleus to the ID of an adjacent
+    cell that *does* contain a nucleus.
+
+    Parameters
+    ----------
+    adj_cell_mask : np.ndarray
+        Labelled (0 = background) cell mask after all other merging steps.
+    nuclei_mask : np.ndarray
+        Labelled (0 = background) nuclei mask.
+
+    Returns
+    -------
+    np.ndarray
+        Updated cell mask with nucleus-free cells merged into
+        neighbouring nucleus-bearing cells.
+    """
+    out = adj_cell_mask.copy()
+
+    # ----------------------------------------------------------------- #
+    # 1 — Identify which cell IDs contain a nucleus
+    nuc_labels = np.unique(nuclei_mask[nuclei_mask > 0])
+
+    cells_with_nuc = set()
+    for nuc_id in nuc_labels:
+        labels, counts = np.unique(adj_cell_mask[nuclei_mask == nuc_id],
+                                   return_counts=True)
+
+        # drop background (label 0) from *both* arrays
+        keep = labels > 0
+        labels = labels[keep]
+        counts = counts[keep]
+
+        if labels.size:                     # at least one non-zero overlap
+            cells_with_nuc.add(labels[np.argmax(counts)])
+
+    # ----------------------------------------------------------------- #
+    # 2 — Build an adjacency map between neighbouring cell IDs
+    # ----------------------------------------------------------------- #
+    boundaries = find_boundaries(adj_cell_mask, mode="thick")
+    adj_map = defaultdict(set)
+
+    ys, xs = np.where(boundaries)
+    h, w = adj_cell_mask.shape
+    for y, x in zip(ys, xs):
+        src = adj_cell_mask[y, x]
+        if src == 0:
+            continue
+        for dy in (-1, 0, 1):
+            for dx in (-1, 0, 1):
+                ny, nx = y + dy, x + dx
+                if 0 <= ny < h and 0 <= nx < w:
+                    dst = adj_cell_mask[ny, nx]
+                    if dst != 0 and dst != src:
+                        adj_map[src].add(dst)
+
+    # ----------------------------------------------------------------- #
+    # 3 — Relabel nucleus-free cells that touch nucleus-bearing neighbours
+    # ----------------------------------------------------------------- #
+    cells_no_nuc = set(np.unique(adj_cell_mask)) - {0} - cells_with_nuc
+    for cell_id in cells_no_nuc:
+        neighbours = adj_map.get(cell_id, set()) & cells_with_nuc
+        if neighbours:
+            # Choose the first nucleus-bearing neighbour deterministically
+            target = sorted(neighbours)[0]
+            out[out == cell_id] = target
+
+    return out.astype(np.uint16)
+
 def adjust_cell_masks(parasite_folder, cell_folder, nuclei_folder, overlap_threshold=5, perimeter_threshold=30):
 
     """
@@ -4541,12 +4613,12 @@ def adjust_cell_masks(parasite_folder, cell_folder, nuclei_folder, overlap_thres
         parasite_mask = np.load(parasite_path, allow_pickle=True)
         cell_mask = np.load(cell_path, allow_pickle=True)
         nuclei_mask = np.load(nuclei_path, allow_pickle=True)
+        
         # Merge and relabel cells
         merged_cell_mask = _merge_cells_based_on_parasite_overlap(parasite_mask, cell_mask, nuclei_mask, overlap_threshold, perimeter_threshold)
         
-        # Force 16 bit
-        #merged_cell_mask = merged_cell_mask.astype(np.uint16)
-        
+        #merged_cell_mask = _merge_cells_without_nucleus(merged_cell_mask, nuclei_mask)
+    
         # Overwrite the original cell mask file with the merged result
         np.save(cell_path, merged_cell_mask)
 
@@ -4836,7 +4908,7 @@ def correct_masks(src):
 
     from .io import _load_and_concatenate_arrays
 
-    cell_path = os.path.join(src,'norm_channel_stack', 'cell_mask_stack')
+    cell_path = os.path.join(src,'masks', 'cell_mask_stack')
     convert_and_relabel_masks(cell_path)
     _load_and_concatenate_arrays(src, [0,1,2,3], 1, 0, 2)
 
@@ -5107,52 +5179,37 @@ def control_filelist(folder, mode='columnID', values=['01','02']):
     return filtered_files
     
 def rename_columns_in_db(db_path):
-    with sqlite3.connect(db_path) as conn:
-        cursor = conn.cursor()
-        
-        # Retrieve all table names in the database
-        cursor.execute("SELECT name FROM sqlite_master WHERE type='table';")
-        tables = [table[0] for table in cursor.fetchall()]
-
-        for table in tables:
-            # Retrieve column names for each table
-            cursor.execute(f"PRAGMA table_info({table});")
-            columns_info = cursor.fetchall()
-            column_names = [col[1] for col in columns_info]
-
-            # Check if columns 'rowID' or 'columnID' exist
-            columns_to_rename = {}
-            if 'row' in column_names:
-                columns_to_rename['row'] = 'rowID'
-            if 'col' in column_names:
-                columns_to_rename['col'] = 'columnID'
-            
-            # Rename columns if necessary
-            if columns_to_rename:
-                # Rename existing table to a temporary name
-                temp_table = f"{table}_old"
-                cursor.execute(f"ALTER TABLE `{table}` RENAME TO `{temp_table}`")
-
-                # Define new columns with updated names
-                column_definitions = ", ".join(
-                    [f"`{columns_to_rename.get(col[1], col[1])}` {col[2]}" for col in columns_info]
-                )
-                cursor.execute(f"CREATE TABLE `{table}` ({column_definitions})")
-                
-                # Copy data to the new table
-                old_columns = ", ".join([f"`{col}`" for col in column_names])
-                new_columns = ", ".join(
-                    [f"`{columns_to_rename.get(col, col)}`" for col in column_names]
-                )
-                cursor.execute(f"INSERT INTO `{table}` ({new_columns}) SELECT {old_columns} FROM `{temp_table}`")
-                try:
-                    cursor.execute(f"DROP TABLE `{temp_table}`")
-                except sqlite3.Error as e:
-                    print(f"Error while dropping temporary table '{temp_table}': {e}")
-
-    # After closing the 'with' block, run VACUUM outside of any transaction
-    with sqlite3.connect(db_path) as conn:
-        conn.execute("VACUUM;")
+    # map old column names → new names
+    rename_map = {
+        'row':      'rowID',
+        'column':   'columnID',
+        'col':      'columnID',
+        'plate':    'plateID',
+        'field':    'fieldID',
+        'channel':  'chanID',
+    }
+
+    con = sqlite3.connect(db_path)
+    cur = con.cursor()
+
+    # 1) get all user tables
+    cur.execute("SELECT name FROM sqlite_master WHERE type='table';")
+    tables = [row[0] for row in cur.fetchall()]
+
+    for table in tables:
+        # 2) get column names only
+        cur.execute(f"PRAGMA table_info(`{table}`);")
+        cols = [row[1] for row in cur.fetchall()]
+
+        # 3) for each old→new, if the old exists and new does not, rename it
+        for old, new in rename_map.items():
+            if old in cols and new not in cols:
+                sql = f"ALTER TABLE `{table}` RENAME COLUMN `{old}` TO `{new}`;"
+                cur.execute(sql)
+                print(f"Renamed `{table}`.`{old}` → `{new}`")
+
+    con.commit()
+    con.close()    
         
 def group_feature_class(df, feature_groups=['cell', 'cytoplasm', 'nucleus', 'pathogen'], name='compartment'):
 
@@ -5189,7 +5246,7 @@ def delete_intermedeate_files(settings):
     path_orig = os.path.join(settings['src'], 'orig')
     path_stack = os.path.join(settings['src'], 'stack')
     merged_stack = os.path.join(settings['src'], 'merged')
-    path_norm_chan_stack = os.path.join(settings['src'], 'norm_channel_stack')
+    path_norm_chan_stack = os.path.join(settings['src'], 'masks')
     path_1 = os.path.join(settings['src'], '1')
     path_2 = os.path.join(settings['src'], '2')
     path_3 = os.path.join(settings['src'], '3')
@@ -5476,3 +5533,37 @@ def correct_metadata(df):
         df = df.rename(columns={'field_name': 'fieldID'})
     
     return df
+
+def remove_outliers_by_group(df, group_col, value_col, method='iqr', threshold=1.5):
+    """
+    Removes outliers from `value_col` within each group defined by `group_col`.
+
+    Parameters:
+        df (pd.DataFrame): The input DataFrame.
+        group_col (str): Column name to group by.
+        value_col (str): Column containing values to check for outliers.
+        method (str): 'iqr' or 'zscore'.
+        threshold (float): Threshold multiplier for IQR (default 1.5) or z-score.
+
+    Returns:
+        pd.DataFrame: A DataFrame with outliers removed.
+    """
+    def iqr_filter(subdf):
+        q1 = subdf[value_col].quantile(0.25)
+        q3 = subdf[value_col].quantile(0.75)
+        iqr = q3 - q1
+        lower = q1 - threshold * iqr
+        upper = q3 + threshold * iqr
+        return subdf[(subdf[value_col] >= lower) & (subdf[value_col] <= upper)]
+
+    def zscore_filter(subdf):
+        mean = subdf[value_col].mean()
+        std = subdf[value_col].std()
+        return subdf[(subdf[value_col] - mean).abs() <= threshold * std]
+
+    if method == 'iqr':
+        return df.groupby(group_col, group_keys=False).apply(iqr_filter)
+    elif method == 'zscore':
+        return df.groupby(group_col, group_keys=False).apply(zscore_filter)
+    else:
+        raise ValueError("method must be 'iqr' or 'zscore'")

{spacr-0.5.0.dist-info → spacr-0.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.5.0
+Version: 0.9.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -10,75 +10,75 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: numpy<2.0,>=1.26.4
-Requires-Dist: pandas<3.0,>=2.2.1
-Requires-Dist: scipy<2.0,>=1.12.0
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-Requires-Dist: scikit-image<1.0,>=0.22.0
-Requires-Dist: scikit-learn<2.0,>=1.4.1
-Requires-Dist: scikit-posthocs<0.20,>=0.10.0
-Requires-Dist: mahotas<2.0,>=1.4.13
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-Requires-Dist: torch<3.0,>=2.0
-Requires-Dist: torchvision<1.0,>=0.1
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+Requires-Dist: nd2reader <4.0,>=3.3.0
 Requires-Dist: czifile
-Requires-Dist: pylibCZIrw<6.0,>=5.0.0
+Requires-Dist: pylibCZIrw <6.0,>=5.0.0
 Requires-Dist: aicspylibczi
 Requires-Dist: readlif
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 Requires-Dist: gdown
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 Requires-Dist: ipykernel
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 Provides-Extra: dev
-Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
+Requires-Dist: pytest <3.11,>=3.9 ; extra == 'dev'
 Provides-Extra: full
-Requires-Dist: opencv-python; extra == "full"
+Requires-Dist: opencv-python ; extra == 'full'
 Provides-Extra: headless
-Requires-Dist: opencv-python-headless; extra == "headless"
+Requires-Dist: opencv-python-headless ; extra == 'headless'
 
 .. |Documentation Status| image:: https://readthedocs.org/projects/spacr/badge/?version=latest
    :target: https://einarolafsson.github.io/spacr

spacr-0.9.1.dist-info/RECORD

@@ -0,0 +1,109 @@
+spacr/__init__.py,sha256=EoGInYks0M4foZElYNhksrQK6aEO1au7cncWexWNhRw,1376
+spacr/__main__.py,sha256=H4MjaMF9ohZL6xfl1kTxVn1Nt_vEhhZArENMMBv8f4E,77
+spacr/app_annotate.py,sha256=W9eLPa_LZIvXsXx_-0iDFEU938LBDvRy6prXo0qF4KQ,2533
+spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
+spacr/app_make_masks.py,sha256=pqDhRpluiHZz-kPX2Zh_KbYe4TsU43qYBa_7f-rsjpw,1694
+spacr/app_mask.py,sha256=l-dBY8ftzCMdDe6-pXc2Nh_u-idNL9G7UOARiLJBtds,153
+spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
+spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
+spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
+spacr/chat_bot.py,sha256=n3Fhqg3qofVXHmh3H9sUcmfYy9MmgRnr48663MVdY9E,1244
+spacr/core.py,sha256=w4E3Pg-ZnA8BOK0iUMTjiNO0GeR5YCEs8fUTbESzqjY,47392
+spacr/deep_spacr.py,sha256=055tIo3WP3elGFiIuSZaLURgu2XyUDxAdbw5ezASEqM,54526
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{spacr-0.5.0.dist-info → spacr-0.9.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.2.0)
+Generator: setuptools (72.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

spacr/resources/MEDIAR/.gitignore

@@ -1,18 +0,0 @@
-config/
-*.log
-*.ipynb
-*.ipynb_checkpoints/
-__pycache__/
-results/
-weights/
-wandb/
-data/
-submissions/
-/.vscode
-*.npy
-*.pth
-*.sh
-*.json
-*.out
-*.zip
-*.tiff

spacr/resources/MEDIAR/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2022 opcrisis
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.