From 78c5db031a3d2ad1d957827c3493a0aeae4b89e9 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Fri, 14 Oct 2022 15:31:00 +0200 Subject: [PATCH] Added image name and recording datetime to the results This two columns where added: - Analysis.Image - Analysis.Datetime When parsing a folder, the image names and (if available) the date and time of the recording is added to the resulting data frame. If the recording datetime is not available, the resulting column will contain NaN --- README.md | 2 +- ...307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xml | 148744 +++++++++++++++ ...307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xsl | 118 + ...SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01.xml | 9297 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_2.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_3.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_4.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A02_1.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A02_2.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A02_3.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A02_4.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A03_1.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A03_2.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A03_3.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A03_4.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A04_1.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A04_2.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A04_3.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A04_4.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B01_1.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B01_2.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B01_3.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B01_4.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B02_1.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B02_2.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B02_3.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B02_4.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B03_1.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B03_2.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B03_3.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B03_4.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B04_1.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B04_2.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B04_3.csv | 101 + ...0801_CHECK-01_SL1,11,9,14_MS_1_1_B04_4.csv | 101 + src/sensospot_parser/__init__.py | 2 +- src/sensospot_parser/columns.py | 4 + src/sensospot_parser/parser.py | 4 + src/sensospot_parser/recordtime.py | 102 + tests/conftest.py | 1 + tests/test_parser.py | 27 +- tests/test_recordtime.py | 98 + 43 files changed, 161627 insertions(+), 4 deletions(-) create mode 100644 example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xml create mode 100644 example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xsl create mode 100644 example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01.xml create mode 100644 example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.csv create mode 100644 example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_2.csv create mode 100644 example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_3.csv create mode 100644 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100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ There is no affiliation on my side regarding Sensovation or Miltenyi, I just use raw_data = sensospot_parser.parse_folder() sorted(raw_data.columns) == [ - 'Analysis.Name', + 'Analysis.Datetime', 'Analysis.Image', 'Analysis.Name', 'Bkg.Area', 'Bkg.Mean', 'Bkg.Median', 'Bkg.StdDev', 'Bkg.Sum', 'Exposure.Id', 'Parameters.Channel', 'Parameters.Time', diff --git a/example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xml b/example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xml new file mode 100644 index 0000000..fe37c69 --- /dev/null +++ b/example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xml @@ -0,0 +1,148744 @@ + + + + 3/7/2022 5:31:40 PM + 3/7/2022 5:33:45 PM + + + + + + + Cy3/Cy5 Green + 3/7/2022 5:31:47 PM + 220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.tif + 150.3716670323235 + 150.6109 + + 150.66990076589988 + -0.62607054037768517 + 0.62607054037768517 + 150.66990076589988 + 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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