diff --git a/pharmbio/data_processing/__pycache__/feature_aggregation.cpython-38.pyc b/pharmbio/data_processing/__pycache__/feature_aggregation.cpython-38.pyc deleted file mode 100644 index 14696d4..0000000 Binary files a/pharmbio/data_processing/__pycache__/feature_aggregation.cpython-38.pyc and /dev/null differ diff --git a/pharmbio/data_processing/__pycache__/quality_control.cpython-38.pyc b/pharmbio/data_processing/__pycache__/quality_control.cpython-38.pyc index 873bdbf..cc09770 100644 Binary files a/pharmbio/data_processing/__pycache__/quality_control.cpython-38.pyc and b/pharmbio/data_processing/__pycache__/quality_control.cpython-38.pyc differ diff --git a/pharmbio/data_processing/quality_control.py b/pharmbio/data_processing/quality_control.py index 8942dae..bc8be05 100644 --- 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 index 8f40532..6f74f76 100644 Binary files a/pharmbio/database/__pycache__/queries.cpython-38.pyc and b/pharmbio/database/__pycache__/queries.cpython-38.pyc differ diff --git a/pharmbio/dataset/__pycache__/cell_morphology.cpython-38.pyc b/pharmbio/dataset/__pycache__/cell_morphology.cpython-38.pyc deleted file mode 100644 index c9382ce..0000000 Binary files a/pharmbio/dataset/__pycache__/cell_morphology.cpython-38.pyc and /dev/null differ diff --git a/pharmbio/dataset/__pycache__/image_quality.cpython-38.pyc b/pharmbio/dataset/__pycache__/image_quality.cpython-38.pyc index 6e4cc5e..4ae5288 100644 Binary files a/pharmbio/dataset/__pycache__/image_quality.cpython-38.pyc and b/pharmbio/dataset/__pycache__/image_quality.cpython-38.pyc differ diff --git a/pharmbio/visualization/__pycache__/__init__.cpython-38.pyc b/pharmbio/visualization/__pycache__/__init__.cpython-38.pyc deleted file mode 100644 index 7af8c1d..0000000 Binary files a/pharmbio/visualization/__pycache__/__init__.cpython-38.pyc and /dev/null differ diff --git a/pharmbio/visualization/__pycache__/plots.cpython-38.pyc b/pharmbio/visualization/__pycache__/plots.cpython-38.pyc deleted file mode 100644 index 19b50d6..0000000 Binary files a/pharmbio/visualization/__pycache__/plots.cpython-38.pyc and /dev/null differ diff --git a/test_package.ipynb b/test_package.ipynb index af8ba94..0c4d735 100644 --- 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))" ] }, {