spacr 0.3.37__py3-none-any.whl → 0.3.38__py3-none-any.whl

spacr/plot.py

@@ -2152,10 +2152,12 @@ class spacrGraph:
     def preprocess_data(self):
         """Preprocess the data: remove NaNs, sort/order the grouping column, and optionally group by 'prc'."""
         # Remove NaNs in both the grouping column and each data column
-        df = self.df.dropna(subset=[self.grouping_column] + self.data_column)  # Handle multiple data columns
+        df = self.df.dropna(subset=[self.grouping_column] + self.data_column)
         # Group by 'prc' column if representation is 'well'
         if self.representation == 'well':
             df = df.groupby(['prc', self.grouping_column])[self.data_column].agg(self.summary_func).reset_index()
+        if self.representation == 'plate':
+            df = df.groupby(['plate', self.grouping_column])[self.data_column].agg(self.summary_func).reset_index()
         if self.order:
             df[self.grouping_column] = pd.Categorical(df[self.grouping_column], categories=self.order, ordered=True)
         else:
@@ -2653,6 +2655,10 @@ def plot_data_from_db(settings):
 
     df = df.dropna(subset=settings['column_name'])
     df = df.dropna(subset=settings['grouping_column'])
+
+
+
+
     #display(df)
 
     #df['class'] = df['png_path'].apply(lambda x: 'class_1' if 'class_1' in x else ('class_0' if 'class_0' in x else None))

spacr/utils.py

@@ -5047,6 +5047,7 @@ def add_column_to_database(settings):
     """
     Adds a new column to the database table by matching on a common column from the DataFrame.
     If the column already exists in the database, it adds the column with a suffix.
+    NaN values will remain as NULL in the database.
     
     Parameters:
     - settings: A dictionary containing the following keys:
@@ -5060,7 +5061,7 @@ def add_column_to_database(settings):
     # Read the DataFrame from the provided CSV path
     df = pd.read_csv(settings['csv_path'])
 
-    # Check for any 0 values in the update column and replace them with 2
+    # Replace 0 values with 2 in the update column
     if (df[settings['update_column']] == 0).any():
         print("Replacing all 0 values with 2 in the update column.")
         df[settings['update_column']].replace(0, 2, inplace=True)
@@ -5073,12 +5074,10 @@ def add_column_to_database(settings):
     cursor.execute(f"PRAGMA table_info({settings['table_name']})")
     columns_in_db = [col[1] for col in cursor.fetchall()]
 
-    # Check if the update column already exists in the database
+    # Add a suffix if the update column already exists in the database
     if settings['update_column'] in columns_in_db:
-        # Add a suffix to the column name (e.g., '_new', '_1', or similar)
         suffix = 1
         new_column_name = f"{settings['update_column']}_{suffix}"
-        # Ensure uniqueness by incrementing the suffix if needed
         while new_column_name in columns_in_db:
             suffix += 1
             new_column_name = f"{settings['update_column']}_{suffix}"
@@ -5086,8 +5085,8 @@ def add_column_to_database(settings):
     else:
         new_column_name = settings['update_column']
 
-    # Add the new column to the database table
-    cursor.execute(f"ALTER TABLE {settings['table_name']} ADD COLUMN {new_column_name} TEXT")
+    # Add the new column with INTEGER type to the database table
+    cursor.execute(f"ALTER TABLE {settings['table_name']} ADD COLUMN {new_column_name} INTEGER")
     print(f"Added new column '{new_column_name}' to the table '{settings['table_name']}'.")
 
     # Iterate over the DataFrame and update the new column in the database
@@ -5095,6 +5094,10 @@ def add_column_to_database(settings):
         value_to_update = row[settings['update_column']]
         match_value = row[settings['match_column']]
 
+        # Handle NaN values by converting them to None (SQLite equivalent of NULL)
+        if pd.isna(value_to_update):
+            value_to_update = None
+
         # Prepare and execute the SQL update query
         query = f"""
             UPDATE {settings['table_name']}
@@ -5107,7 +5110,4 @@ def add_column_to_database(settings):
     conn.commit()
     conn.close()
 
-    print(f"Updated '{new_column_name}' in '{settings['table_name']}' using '{settings['match_column']}'.")
-
-
-
+    print(f"Updated '{new_column_name}' in '{settings['table_name']}' using '{settings['match_column']}'.")

{spacr-0.3.37.dist-info → spacr-0.3.38.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.37
+Version: 0.3.38
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.3.37.dist-info → spacr-0.3.38.dist-info}/RECORD

@@ -20,14 +20,14 @@ spacr/measure.py,sha256=BThn_sALgKrwGKnLOGpT4FyoJeRVoTZoP9SXbCtCMRw,54857
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
 spacr/ml.py,sha256=ItibDL_q0cKwEsJdwpBtVqfpRQGPXGbb0BX5UB5iH5s,49342
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=QYj2bV0-6UqKRTWeSj3eOOgr6dNMmCCc4TdRGTniQ4c,118083
+spacr/plot.py,sha256=W6F2Jaxq7WBnB9G3-7AESdQs6foGeyS70-LZwKgKJv8,118214
 spacr/sequencing.py,sha256=t18mgpK6rhWuB1LtFOsPxqgpFXxuUmrD06ecsaVQ0Gw,19655
 spacr/settings.py,sha256=AzP9NGiXI1MqT69bHObxwDSCUk0kdstBVvl1JpcD_-w,75960
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
 spacr/submodules.py,sha256=AB7s6-cULsaqz-haAaCtXfGEIi8uPZGT4xoCslUJC3Y,18391
 spacr/timelapse.py,sha256=FSYpUtAVy6xc3lwprRYgyDTT9ysUhfRQ4zrP9_h2mvg,39465
 spacr/toxo.py,sha256=us3pQyULtMTyfTq0MWPn4QJTTmQ6BwAJKChNf75jo3I,10082
-spacr/utils.py,sha256=3SBf5yeeU3u9MVsIWeYmcHjhwqs8LJ6m9UF0wBSNq8M,216304
+spacr/utils.py,sha256=j6qE7aTGu7D82_A68md5b5Vgn8UrW2w2saa6nCbANw8,216373
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
 spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
@@ -150,9 +150,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.3.37.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.3.37.dist-info/METADATA,sha256=Y65Rn3Py1AHsgydWiBFLsd0_vPVhxubiYizcIpfFIbE,5949
-spacr-0.3.37.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.3.37.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.3.37.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.3.37.dist-info/RECORD,,
+spacr-0.3.38.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.3.38.dist-info/METADATA,sha256=IfwGcod8ZUdemPlpbdoCoONBap_IZQCfiL-KURN3KuI,5949
+spacr-0.3.38.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.3.38.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.3.38.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.3.38.dist-info/RECORD,,