fixed quality_control pl.max() issues

pharmbio · Sep 28, 2023 · fe594f0 · fe594f0
1 parent 55baad4
commit fe594f0
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Showing 9 changed files with 6 additions and 14 deletions.
diff --git a/pharmbio/data_processing/__pycache__/feature_aggregation.cpython-38.pyc b/pharmbio/data_processing/__pycache__/feature_aggregation.cpython-38.pyc
diff --git a/pharmbio/data_processing/__pycache__/quality_control.cpython-38.pyc b/pharmbio/data_processing/__pycache__/quality_control.cpython-38.pyc
diff --git a/pharmbio/data_processing/quality_control.py b/pharmbio/data_processing/quality_control.py
@@ -256,7 +256,7 @@ def flag_outlier_images(
             item for item in qc_data.columns if item.startswith(outlier_prefix)
         ]
         flagged_qc_data = qc_data.with_columns(
-            pl.max(pl.col(outlier_flaged_columns)).alias("outlier_flag")
+            pl.max_horizontal(outlier_flaged_columns).alias("outlier_flag")
         )
 
     elif method == "IQR":
@@ -298,6 +298,7 @@ def flag_outlier_images(
         outlier_flaged_columns = [
             item for item in qc_data.columns if item.startswith(outlier_prefix)
         ]
+        print("New code reached")
         flagged_qc_data = qc_data.with_columns(
             pl.max_horizontal(outlier_flaged_columns).alias("outlier_flag")
         )

diff --git a/pharmbio/database/__pycache__/queries.cpython-38.pyc b/pharmbio/database/__pycache__/queries.cpython-38.pyc
diff --git a/pharmbio/dataset/__pycache__/cell_morphology.cpython-38.pyc b/pharmbio/dataset/__pycache__/cell_morphology.cpython-38.pyc
diff --git a/pharmbio/dataset/__pycache__/image_quality.cpython-38.pyc b/pharmbio/dataset/__pycache__/image_quality.cpython-38.pyc
diff --git a/pharmbio/visualization/__pycache__/__init__.cpython-38.pyc b/pharmbio/visualization/__pycache__/__init__.cpython-38.pyc
diff --git a/pharmbio/visualization/__pycache__/plots.cpython-38.pyc b/pharmbio/visualization/__pycache__/plots.cpython-38.pyc
diff --git a/test_package.ipynb b/test_package.ipynb
@@ -104,17 +104,8 @@
    "source": [
     "from pharmbio.dataset.image_quality import get_image_quality_ref, get_image_quality_data\n",
     "\n",
-    "qc_ref_df = get_image_quality_ref(\"specs3k\")\n",
-    "qc_df = get_image_quality_data(qc_ref_df, force_merging_columns='drop')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "qc_df"
+    "qc_ref_df = get_image_quality_ref(\"specs3k\", filter={'plate_barcode': ['P101334']})\n",
+    "qc_df = get_image_quality_data(qc_ref_df)"
    ]
   },
   {
@@ -145,8 +136,8 @@
     "df = qc_df\n",
     "# get_qc_module(df)\n",
     "# get_channels(df, out_put='print')\n",
-    "flag_outlier_images(qc_df)\n",
-    "# flag_outlier_images(df)"
+    "# flag_outlier_images(qc_df)\n",
+    "# flag_outlier_images(df, method='SD', default_sd_step=(-4.5, 4.5))"
    ]
   },
   {