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a/src/sensospot_parser/__init__.py b/src/sensospot_parser/__init__.py index a01faca..1ad604a 100644 --- a/src/sensospot_parser/__init__.py +++ b/src/sensospot_parser/__init__.py @@ -3,7 +3,7 @@ Parsing the numerical output from Sensovations Sensospot image analysis. """ -__version__ = "0.8.1" +__version__ = "0.9.0" import sys diff --git a/src/sensospot_parser/columns.py b/src/sensospot_parser/columns.py index a2bc03d..9897d32 100644 --- a/src/sensospot_parser/columns.py +++ b/src/sensospot_parser/columns.py @@ -32,6 +32,8 @@ CSV_RENAME_MAP = { # meta data extracted from filename and path ANALYSIS_NAME = "Analysis.Name" +ANALYSIS_IMAGE = "Analysis.Image" +ANALYSIS_DATETIME = "Analysis.Datetime" EXPOSURE_ID = "Exposure.Id" WELL_NAME = "Well.Name" WELL_ROW = "Well.Row" @@ -44,6 +46,8 @@ PARAMETERS_CHANNEL = "Parameters.Channel" PARSED_DATA_COLUMN_SET = { ANALYSIS_NAME, + ANALYSIS_IMAGE, + ANALYSIS_DATETIME, WELL_NAME, WELL_ROW, WELL_COLUMN, diff --git a/src/sensospot_parser/parser.py b/src/sensospot_parser/parser.py index f5f278f..799afa5 100644 --- a/src/sensospot_parser/parser.py +++ b/src/sensospot_parser/parser.py @@ -12,6 +12,7 @@ import pandas from . import columns from .parameters import add_measurement_parameters +from .recordtime import add_record_time PathLike = Union[str, pathlib.Path] @@ -123,6 +124,7 @@ def parse_file(data_file: PathLike) -> pandas.DataFrame: data_frame[columns.WELL_COLUMN] = measurement_info.column data_frame[columns.EXPOSURE_ID] = measurement_info.exposure data_frame[columns.ANALYSIS_NAME] = data_path.parent.name + data_frame[columns.ANALYSIS_IMAGE] = data_path.with_suffix(".tif").name return _cleanup_data_columns(data_frame) @@ -224,6 +226,8 @@ def parse_folder(folder: PathLike, quiet: bool = False) -> pandas.DataFrame: except ValueError: raise ValueError(f"No sensospot data found in folder '{folder}'") data_frame = add_measurement_parameters(data_frame, folder_path) + data_frame = add_record_time(data_frame, folder_path) + print(data_frame) if quiet: return data_frame return _sanity_check(data_frame) diff --git a/src/sensospot_parser/recordtime.py b/src/sensospot_parser/recordtime.py new file mode 100644 index 0000000..7d7c721 --- /dev/null +++ b/src/sensospot_parser/recordtime.py @@ -0,0 +1,102 @@ +""" Sensospot Data Parser + +Parsing the numerical output from Sensovations Sensospot image analysis. +""" + +import pathlib +from typing import Tuple, Union, Iterable, Optional + +import numpy +import pandas +from defusedxml import ElementTree + +from . import columns + +PathLike = Union[str, pathlib.Path] + + +def _search_records_file(folder: PathLike) -> Optional[pathlib.Path]: + """searches for a the records xml file in a folder + + Args: + folder: directory to search + + Returns: + the path to the settings file or None + """ + folder_path = pathlib.Path(folder) + files = (item for item in folder_path.iterdir() if item.suffix == ".xsl") + xls_files = [path for path in files if not path.name.startswith(".")] + if len(xls_files) == 1: + xml_file = xls_files[0].with_suffix(".xml") + if xml_file.is_file(): + return xml_file + return None + + +def _iter_records(records_file: PathLike) -> Iterable[Tuple[str, str]]: + """parses the information from a records file + + Args: + records_file: path to the records file + + Yields: + tuples, filename as first element and the datetime string as second + """ + records_path = pathlib.Path(records_file) + tree = ElementTree.parse(records_path) + for channel_config in tree.findall(".//*[ImageFileName]"): + image_tag = channel_config.find("ImageFileName") + image_name = None if image_tag is None else image_tag.text + datetime_tag = channel_config.find("Timestamp") + datetime_str = None if datetime_tag is None else datetime_tag.text + yield image_name, datetime_str + + +def _parse_records_file(records_file: PathLike) -> pandas.DataFrame: + """parses the information from a records file + + Args: + records_file: path to the records file + + Returns: + pandas data frame with the parsed information + """ + data = _iter_records(records_file) + data_frame = pandas.DataFrame( + data, columns=[columns.ANALYSIS_IMAGE, columns.ANALYSIS_DATETIME] + ) + data_frame[columns.ANALYSIS_DATETIME] = pandas.to_datetime( + data_frame[columns.ANALYSIS_DATETIME] + ) + return data_frame + + +def add_record_time( + measurement: pandas.DataFrame, folder: PathLike +) -> pandas.DataFrame: + """adds the recoding datetime to the data frame + + The returned DataFrame will contain one more column for parsed datetime + + If the parameters could not be foundor do not match up with the + measurement data, the additional collumn will contain NaN. + + Argumentss: + measurement: the parsed measurement data + folder: the folder of the measurement data + + Returns: + the measurement data with parameters added + """ + record_path = _search_records_file(folder) + print(f"PATH: {record_path}") + if record_path is None: + print("assuming record path is None") + measurement[columns.ANALYSIS_DATETIME] = numpy.NAN + return measurement + + data_frame = _parse_records_file(record_path) + print(data_frame) + print(measurement[columns.ANALYSIS_IMAGE].iloc[0]) + return measurement.merge(data_frame, how="left", on=columns.ANALYSIS_IMAGE) diff --git a/tests/conftest.py b/tests/conftest.py index e2ba728..19d2ce6 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -7,6 +7,7 @@ import pytest EXAMPLE_DIR_WO_PARAMS = "mtp_wo_parameters" EXAMPLE_DIR_WITH_PARAMS = "mtp_with_parameters" +EXAMPLE_DIR_WITH_RECORD = "record_time" @pytest.fixture(scope="session") diff --git a/tests/test_parser.py b/tests/test_parser.py index 785e612..c9659b1 100644 --- a/tests/test_parser.py +++ b/tests/test_parser.py @@ -4,7 +4,11 @@ import numpy import pytest -from .conftest import EXAMPLE_DIR_WO_PARAMS, EXAMPLE_DIR_WITH_PARAMS +from .conftest import ( + EXAMPLE_DIR_WO_PARAMS, + EXAMPLE_DIR_WITH_PARAMS, + EXAMPLE_DIR_WITH_RECORD, +) @pytest.mark.parametrize( @@ -173,6 +177,7 @@ def test_parse_file(example_file): "Well.Column", "Exposure.Id", "Analysis.Name", + "Analysis.Image", } assert set(result.columns) == columns @@ -181,6 +186,8 @@ def test_parse_file(example_file): assert result["Well.Column"][0] == 1 assert result["Exposure.Id"][0] == 1 assert result["Analysis.Name"][0] == "mtp_wo_parameters" + file_name = "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.tif" + assert result["Analysis.Image"][0] == file_name def test_parse_file_raises_error(example_dir): @@ -267,7 +274,7 @@ def test_find_csv_files(example_dir): assert all(not item.stem.startswith(".") for item in result) -def test_parse_folder(example_dir): +def test_parse_folder_no_datetime_records(example_dir): from sensospot_parser.parser import parse_folder data_frame = parse_folder(example_dir / EXAMPLE_DIR_WITH_PARAMS) @@ -279,6 +286,22 @@ def test_parse_folder(example_dir): assert len(data_frame["Pos.Id"].unique()) == 100 assert len(data_frame["Parameters.Channel"].unique()) == 2 assert len(data_frame["Parameters.Time"].unique()) == 3 + assert len(data_frame["Analysis.Datetime"].unique()) == 1 + + +def test_parse_folder_with_datetime_records(example_dir): + from sensospot_parser.parser import parse_folder + + data_frame = parse_folder(example_dir / EXAMPLE_DIR_WITH_RECORD) + + assert len(data_frame) == 8 * 4 * 100 + assert len(data_frame["Well.Row"].unique()) == 2 + assert len(data_frame["Well.Column"].unique()) == 4 + assert len(data_frame["Exposure.Id"].unique()) == 4 + assert len(data_frame["Pos.Id"].unique()) == 100 + assert len(data_frame["Parameters.Channel"].unique()) == 1 + assert len(data_frame["Parameters.Time"].unique()) == 1 + assert len(data_frame["Analysis.Datetime"].unique()) == 8 def test_sanity_check_ok(example_dir): diff --git a/tests/test_recordtime.py b/tests/test_recordtime.py new file mode 100644 index 0000000..6a998da --- /dev/null +++ b/tests/test_recordtime.py @@ -0,0 +1,98 @@ +import pandas +import pytest + +from .conftest import EXAMPLE_DIR_WITH_PARAMS, EXAMPLE_DIR_WITH_RECORD + + +@pytest.fixture +def file_list(example_dir): + import pathlib + + path = pathlib.Path(example_dir / EXAMPLE_DIR_WITH_RECORD) + tifs = (i.with_suffix(".tif") for i in path.glob("*.csv")) + return [i.name for i in tifs] + + +def test_search_records_file_ok(example_dir): + from sensospot_parser.recordtime import _search_records_file + + result = _search_records_file(example_dir / EXAMPLE_DIR_WITH_RECORD) + + assert result.suffix == ".xml" + + +def test_search_records_file_not_found(example_dir): + from sensospot_parser.recordtime import _search_records_file + + result = _search_records_file(example_dir / EXAMPLE_DIR_WITH_PARAMS) + + assert result is None + + +def test_iter_records(example_dir): + from sensospot_parser.recordtime import _iter_records, _search_records_file + + path = _search_records_file(example_dir / EXAMPLE_DIR_WITH_RECORD) + + result = list(_iter_records(path)) + + assert ( + result[0][0] == "220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.tif" + ) + assert result[0][1] == "3/7/2022 5:31:47 PM" + assert ( + result[-1][0] == "220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_D04_4.tif" + ) + assert result[-1][1] == "3/7/2022 5:33:41 PM" + + +def test_parse_records_file(example_dir): + from sensospot_parser.recordtime import ( + _parse_records_file, + _search_records_file, + ) + + path = _search_records_file(example_dir / EXAMPLE_DIR_WITH_RECORD) + + result = _parse_records_file(path) + + assert isinstance(result, pandas.DataFrame) + assert list(result.columns) == ["Analysis.Image", "Analysis.Datetime"] + assert len(result) == 64 + + +def test_add_record_time_ok(example_dir, file_list): + from sensospot_parser.recordtime import add_record_time + + df = pandas.DataFrame(file_list, columns=["Analysis.Image"]) + + result = add_record_time(df, example_dir / EXAMPLE_DIR_WITH_RECORD) + + assert len(df) == len(result) + assert list(result.columns) == ["Analysis.Image", "Analysis.Datetime"] + assert not result["Analysis.Datetime"].hasnans + + +def test_add_record_time_unknown_file(example_dir, file_list): + from sensospot_parser.recordtime import add_record_time + + extended_list = file_list + ["unknown file"] + df = pandas.DataFrame(extended_list, columns=["Analysis.Image"]) + + result = add_record_time(df, example_dir / EXAMPLE_DIR_WITH_RECORD) + + assert len(df) == len(result) + assert list(result.columns) == ["Analysis.Image", "Analysis.Datetime"] + assert result["Analysis.Datetime"].hasnans + + +def test_add_record_time_no_record_xml(example_dir, file_list): + from sensospot_parser.recordtime import add_record_time + + df = pandas.DataFrame(file_list, columns=["Analysis.Image"]) + + result = add_record_time(df, example_dir / EXAMPLE_DIR_WITH_PARAMS) + + assert len(df) == len(result) + assert list(result.columns) == ["Analysis.Image", "Analysis.Datetime"] + assert result["Analysis.Datetime"].hasnans