diff --git a/sensospot_data/__init__.py b/sensospot_data/__init__.py index a6f155d..062b1cb 100644 --- a/sensospot_data/__init__.py +++ b/sensospot_data/__init__.py @@ -12,9 +12,8 @@ from pathlib import Path import click import pandas -from . import columns +from . import columns # noqa: F401 from .parser import parse_file, parse_folder # noqa: F401 -from .parameters import ExposureInfo # noqa: F401 DEFAULT_OUTPUT_FILENAME = "collected_data.csv" diff --git a/sensospot_data/parameters.py b/sensospot_data/parameters.py index d714459..1d09d68 100644 --- a/sensospot_data/parameters.py +++ b/sensospot_data/parameters.py @@ -12,7 +12,6 @@ from defusedxml import ElementTree from . import columns -ExposureInfo = namedtuple("ExposureInfo", ["channel", "time"]) def _search_measurement_params_file(folder): @@ -28,21 +27,28 @@ def _search_measurement_params_file(folder): return None +def _get_channel_data(channel_node): + # child.tag == "ChannelConfig1" + exposure_id = int(channel_node.tag[-1]) + # channel_description == "[Cy3|Cy5] Green" + description = channel_node.attrib["Description"] + exposure_channel = description.rsplit(" ", 1)[-1] + # floats can be used for exposure times, not only ints + exposure_time = float(channel_node.attrib["ExposureTimeMs"]) + return { + columns.EXPOSURE_ID: exposure_id, + columns.PARAMETERS_CHANNEL: exposure_channel.lower(), + columns.PARAMETERS_TIME: exposure_time, + } + + def _parse_measurement_params(params_file): """parses the cannel informations from a settings file""" file_path = Path(params_file) with file_path.open("r") as file_handle: tree = ElementTree.parse(file_handle) - result = {} - for child in tree.find("Channels"): - # child.tag == "ChannelConfig1" - exposure = int(child.tag[-1]) - channel_description = child.attrib["Description"] - # channel_description == "[Cy3|Cy5] Green" - channel = channel_description.rsplit(" ", 1)[-1] - time = float(child.attrib["ExposureTimeMs"]) - result[exposure] = ExposureInfo(channel.lower(), time) - return result + data = [_get_channel_data(child) for child in tree.find("Channels")] + return pandas.DataFrame(data) def get_measurement_params(folder): @@ -53,51 +59,16 @@ def get_measurement_params(folder): return None -def _add_measurement_params(data_frame, params): - """adds measurement parameters to a data frame""" - keys = [columns.PARAMETERS_CHANNEL, columns.PARAMETERS_TIME] - map = {k: dict(zip(keys, v)) for k, v in params.items()} - return _apply_map(data_frame, map, columns.EXPOSURE_ID) - - -def _apply_map(data_frame, map, index_col): - """adds a nested dictionary to a data frame on a specific index column - - map: - keys: must be the same as the values in the index column, - values: dictionary with new column names as keys and the values - - example: - - >>> df = DataFrame(data={"MyIndex": [10, 10, 20]}) - >>> map = { - ... 10: {"NewCol": "foo"}, - ... 20: {"NewCol": "Bar"}, - ... } - >>> apply_map(df, map, "MyIndex") - MyIndex NewCol - 0 10 foo - 1 10 foo - 2 20 bar - - """ - map_df = pandas.DataFrame.from_dict(map, orient="index") - return data_frame.merge( - map_df, - how="left", - left_on=index_col, - right_index=True, - ) - - def add_optional_measurement_parameters(data_frame, folder): """adds measurement params to the data frame, if they could be parsed""" params = get_measurement_params(folder) - if params: - available_exposures = set(data_frame[columns.EXPOSURE_ID].unique()) - if available_exposures == set(params.keys()): - return _add_measurement_params(data_frame, params) - else: - data_frame[columns.PARAMETERS_CHANNEL] = numpy.nan - data_frame[columns.PARAMETERS_TIME] = numpy.nan + if params is not None: + params_exposures = params[columns.EXPOSURE_ID].unique() + data_exposures = data_frame[columns.EXPOSURE_ID].unique() + if set(data_exposures) == set(params_exposures): + return data_frame.merge(params, how="left", on=columns.EXPOSURE_ID) + + # only executing if the parameters were not merged to the data frame + data_frame[columns.PARAMETERS_CHANNEL] = numpy.nan + data_frame[columns.PARAMETERS_TIME] = numpy.nan return data_frame diff --git a/sensospot_data/parser.py b/sensospot_data/parser.py index cbe4d12..1b8515a 100755 --- a/sensospot_data/parser.py +++ b/sensospot_data/parser.py @@ -9,9 +9,10 @@ from collections import namedtuple import pandas -from . import columns +from . import columns from .parameters import add_optional_measurement_parameters + REGEX_WELL = re.compile( r""" (?P([A-Z]+)) # row name containing one or more letters diff --git a/tests/test_parameters.py b/tests/test_parameters.py index dc4a7c3..48f2b5c 100644 --- a/tests/test_parameters.py +++ b/tests/test_parameters.py @@ -1,3 +1,4 @@ +import pandas from .conftest import EXAMPLE_DIR_WO_PARAMS, EXAMPLE_DIR_WITH_PARAMS @@ -43,10 +44,13 @@ def test_parse_channel_info(example_dir): ) result = _parse_measurement_params(params) - assert set(result.keys()) == {1, 2, 3} - assert result[1] == ("green", 100) - assert result[2] == ("red", 150) - assert result[3] == ("red", 15) + expected = pandas.DataFrame({ + "Exposure.Id": [1,2,3], + "Parameters.Channel": ["green", "red", "red"], + "Parameters.Time" : [100.0, 150.0, 15.0] + }) + + assert result.equals(expected) def test_get_measurement_params_file_found(example_dir): @@ -54,10 +58,13 @@ def test_get_measurement_params_file_found(example_dir): result = get_measurement_params(example_dir / EXAMPLE_DIR_WITH_PARAMS) - assert set(result.keys()) == {1, 2, 3} - assert result[1] == ("green", 100) - assert result[2] == ("red", 150) - assert result[3] == ("red", 15) + expected = pandas.DataFrame({ + "Exposure.Id": [1,2,3], + "Parameters.Channel": ["green", "red", "red"], + "Parameters.Time" : [100.0, 150.0, 15.0] + }) + + assert result.equals(expected) def test_get_measurement_params_file_not_found(example_dir): @@ -68,28 +75,6 @@ def test_get_measurement_params_file_not_found(example_dir): assert result is None -def test_add_measurement_params(exposure_df): - from sensospot_data.parameters import ExposureInfo, _add_measurement_params - - params = { - 1: ExposureInfo("red", 10), - 2: ExposureInfo("green", 20), - 3: ExposureInfo("blue", 50), - } - - result = _add_measurement_params(exposure_df, params) - - assert result["Exposure.Id"][0] == 1 - assert result["Parameters.Channel"][0] == "red" - assert result["Parameters.Time"][0] == 10 - assert result["Exposure.Id"][1] == 2 - assert result["Parameters.Channel"][1] == "green" - assert result["Parameters.Time"][1] == 20 - assert result["Exposure.Id"][2] == 3 - assert result["Parameters.Channel"][2] == "blue" - assert result["Parameters.Time"][2] == 50 - - def test_add_optional_measurement_parameters_with_params_file( exposure_df, example_dir ): @@ -121,60 +106,3 @@ def test_add_optional_measurement_parameters_without_params_file( assert one_exposure_data_frame["Parameters.Time"].hasnans -def test_apply_map(exposure_df): - from sensospot_data.parameters import _apply_map - - map = { - 1: {"SomeColumn": "A", "OtherColumn": 9}, - 2: {"SomeColumn": "B", "OtherColumn": 8}, - 3: {"SomeColumn": "C", "OtherColumn": 7}, - } - - result = _apply_map(exposure_df, map, "Exposure.Id") - - for key, value in map.items(): - mask = result["Exposure.Id"] == key - partial = result.loc[mask] - assert set(partial["SomeColumn"].unique()) == {value["SomeColumn"]} - assert set(partial["OtherColumn"].unique()) == {value["OtherColumn"]} - - -def test_apply_map_keys_not_in_df(exposure_df): - from sensospot_data.parameters import _apply_map - - map = { - 1: {"some_col": "A", "other_col": 9}, - 2: {"some_col": "B", "other_col": 8}, - 3: {"some_col": "C", "other_col": 7}, - 4: {"some_col": "D", "other_col": 6}, - } - - result = _apply_map(exposure_df, map, "Exposure.Id") - - for key in (1, 2, 3): - value = map[key] - mask = result["Exposure.Id"] == key - partial = result.loc[mask] - assert set(partial["some_col"].unique()) == {value["some_col"]} - assert set(partial["other_col"].unique()) == {value["other_col"]} - - assert "D" not in set(result["some_col"].unique()) - assert "6" not in set(result["other_col"].unique()) - - -def test_apply_map_not_all_keys_map_to_df(exposure_df): - from sensospot_data.parameters import _apply_map - - map = { - 1: {"some_col": "A", "other_col": 9}, - 3: {"some_col": "C", "other_col": 7}, - } - - result = _apply_map(exposure_df, map, "Exposure.Id") - - assert not result.iloc[0].hasnans - assert result.iloc[1].hasnans - assert not result.iloc[2].hasnans - - assert result["some_col"].hasnans - assert result["other_col"].hasnans diff --git a/tests/test_sensospot_data.py b/tests/test_sensospot_data.py index 967d743..90e4cd6 100644 --- a/tests/test_sensospot_data.py +++ b/tests/test_sensospot_data.py @@ -2,8 +2,7 @@ def test_import_api(): - from sensospot_data import ExposureInfo # noqa: F401 from sensospot_data import main # noqa: F401 + from sensospot_data import columns # noqa: F401 from sensospot_data import parse_file # noqa: F401 from sensospot_data import parse_folder # noqa: F401 - from sensospot_data import columns # noqa: F401