holgi
/
sensospot_parser
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity
Browse Source

renamed some functions in "csv_parser" module to have more explicit names

xmlparsing
Holger Frey 2 years ago
parent
8644a25d78
commit
988c7562d9
8 changed files with 47 additions and 106 deletions
Whitespace
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Split View
Diff Options
Show Stats Download Patch File Download Diff File
  1. 25
      example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svalg
  2. 27
      example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svary
  3. 19
      example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svexp
  4. 4
      src/sensospot_parser/__init__.py
  5. 20
      src/sensospot_parser/csv_parser.py
  6. 8
      tests/conftest.py
  7. 46
      tests/test_csv_parser.py
  8. 4
      tests/test_sensospot_data.py

25
example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svalg
Unescape View File

@ -1,25 +0,0 @@ @@ -1,25 +0,0 @@
<?xml version="1.0" encoding="utf-8"?>
<!--Algorithm configuration-->
<Algorithm>
<BrightnessCheck>
<Settings Active="False" MinimumBrightnessPercent="70" MaximumBrightnessPercent="100" HistogrammPercent="95" OverrideMaximumPixelValue="0" SubSampleX="2" SubSampleY="2" />
</BrightnessCheck>
<Shading>
<Settings Active="true" />
</Shading>
<OrientationDetection>
<Settings Active="True" HoughCircleSensitivitySliderUsed="True" BlobMethod="Classic,HoughCircle" HoughCircleGamma="1.1" HoughCircleScale="1" HoughCircleMinDist="5" HoughCircleCannyThresh="100" HoughCircleAccumThresh="15" HoughCircleMinRadius="5" HoughCircleMaxRadius="30" HoughCircleSmoothRadius="0" HoughCircleDilationRadius="3" HoughCircleSensitivitySlider="2" RefPatternFittingMethod="ICP" BinThresholdPercent="2" JoinRadius="2" OpeningNeighborhoodSizeXY="7" BlobAreaMin="50">
</Settings>
<DebugSettings ImageDebugAODResult="0" ImageDebugAODBinary="0" ImageDebugAODMorphed="1" ShowResults="1" ShowSearchOrder="1" ShowDistances="1" />
</OrientationDetection>
<Flip>
<Settings Direction="FLIP_NONE" />
</Flip>
<MicroArraySpotFinding>
<Settings Active="True" BkgAvgAreaPix="10" HistogramPerCent="10" BinarizationThresholdOffsetPerc="7" SpotImageSubSampling="1" ApertureWidth="3" MinArea="50" MinSpotDiameterMm="0.2" SpotFindingSensitivity="10" SpotShape="CIRCLE" SelectionPreference="COMPACTEST" InsideGridRectCriteria="RECTANGLE" BlobbingActive="True" CircleDetectionActive="True" MeanBeforeEdgeDetectionActive="False" CannyThreshold="50" MinMatchQuality="0.4" CircleMatchExponent="1" />
</MicroArraySpotFinding>
<MicroArrayAnalysis>
<Settings Active="True" MinBkgThresholdPerc="1" MaxSpotThresholdPerc="100" AutoAdjustAnalysisDiameter="False" MinSpotSizeMm="0.2" MaxSpotSizeMm="0.28" AutoAdjustTolerancePercentage="10">
</Settings>
</MicroArrayAnalysis>
</Algorithm>

27
example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svary
Unescape View File

@ -1,27 +0,0 @@ @@ -1,27 +0,0 @@
<?xml version="1.0" encoding="utf-8"?>
<!--Definition of the microarray and the-->
<!--embedded reference pattern-->
<MicroArray>
<Layout NofSpotsX="10" NofSpotsY="10" SpotDistMmX="0.303" SpotDistMmY="0.297" />
<ReferencePattern ReferencePointOffsetMm.X="1.6392982179205673" ReferencePointOffsetMm.Y="2.0253288169139632">
<Features MarkerType="BRIGHT">
</Features>
<Tolerances ScalePercent="5" RotationPercent="5">
<CIRCLE PositionMm="0.06" SizePercent="50" SimpleCompactnessMax="17" EccentricityMax="0.2" />
<RECT PositionMm="0.1" SizePercent="30" SimpleCompactnessMin="13" SimpleCompactnessMax="22" EccentricityMin="0.25" EccentricityMax="0.4">
</RECT>
</Tolerances>
<Shapes>
<Shape0 ShapeType="CIRCLE" PosMm.X="0" PosMm.Y="0" DiameterMm="0.187">
</Shape0>
<Shape1 ShapeType="CIRCLE" PosMm.X="2.728" PosMm.Y="2.682" DiameterMm="0.184">
</Shape1>
<Shape2 ShapeType="CIRCLE" PosMm.X="2.701" PosMm.Y="-0.021" DiameterMm="0.187">
</Shape2>
<Shape3 ShapeType="CIRCLE" PosMm.X="0.024" PosMm.Y="2.7" DiameterMm="0.191">
</Shape3>
</Shapes>
</ReferencePattern>
<RelationArrayToRefPattern OffsetMm.X="0" OffsetMm.Y="0" ScalingFactor="0.99430589150056758" RotationAngleDeg="-0.13126175132547502">
</RelationArrayToRefPattern>
</MicroArray>

19
example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svexp
Unescape View File

@ -1,19 +0,0 @@ @@ -1,19 +0,0 @@
<?xml version="1.0"?>
<Assay>
<Channels>
<ChannelConfig1 IlluminationID="4" Description="Cy3/Cy5 Green" ExposureTimeMs="100" Intensity="100">
</ChannelConfig1>
<ChannelConfig2 IlluminationID="3" Description="Cy3/Cy5 Red" ExposureTimeMs="150" Intensity="100">
</ChannelConfig2>
<ChannelConfig3 IlluminationID="3" Description="Cy3/Cy5 Red" ExposureTimeMs="15" Intensity="100">
</ChannelConfig3>
</Channels>
<Components MicroArray="S QC 10x10 Cy3 100ms Cy5 150-15ms" AlgoConfig="S QC 10x10 Cy3 100ms Cy5 150-15ms">
</Components>
<DebugSwitches DoImageProcessing="True" DoDarkImageCorrection="True" SaveResultAsCSVFile="True" SaveResultAsXmlFile="True">
</DebugSwitches>
<RefPattern ChannelConfig="Channel1">
</RefPattern>
<WorkbookAnalysis Active="True" UseSingleWorkbook="YES" TemplateWorkbookName="160212_wb10x10_Spectra_V3_Ver03.2.3.xlsx" PasteWorksheetName="Input_Data" PasteStartingCell="W300" ParameterWorksheetName="parameter" ResultWorksheetName="Net Intensity" KeepDataWorkbookOpen="NO">
</WorkbookAnalysis>
</Assay>

4
src/sensospot_parser/__init__.py
Unescape View File

@ -12,7 +12,7 @@ import click @@ -12,7 +12,7 @@ import click
import pandas
from . import columns # noqa: F401
from .csv_parser import parse_file, parse_folder # noqa: F401
from .csv_parser import parse_csv_file, parse_csv_folder # noqa: F401
DEFAULT_OUTPUT_FILENAME = "collected_data.csv"
@ -51,7 +51,7 @@ def main(sources, output, quiet=False): @@ -51,7 +51,7 @@ def main(sources, output, quiet=False):
"""
paths = (pathlib.Path(source) for source in sources)
collection = (parse_folder(source, quiet) for source in paths)
collection = (parse_csv_folder(source, quiet) for source in paths)
result = pandas.concat(collection, ignore_index=True).to_csv(
output, sep="\t", index=False
)

20
src/sensospot_parser/csv_parser.py
Unescape View File

@ -84,7 +84,7 @@ def _extract_measurement_info(data_file: PathLike) -> FileInfo: @@ -84,7 +84,7 @@ def _extract_measurement_info(data_file: PathLike) -> FileInfo:
return FileInfo(row, column, exposure)
def parse_file(data_file: PathLike) -> pandas.DataFrame:
def parse_csv_file(data_file: PathLike) -> pandas.DataFrame:
"""parses one data file and adds metadata to result
will race a ValueError, if metadata could not be extracted
@ -113,7 +113,9 @@ def parse_file(data_file: PathLike) -> pandas.DataFrame: @@ -113,7 +113,9 @@ def parse_file(data_file: PathLike) -> pandas.DataFrame:
return columns._cleanup_data_columns(data_frame)
def _parse_file_silenced(data_file: PathLike) -> Optional[pandas.DataFrame]:
def _parse_csv_file_silenced(
data_file: PathLike,
) -> Optional[pandas.DataFrame]:
"""parses one data file and adds metadata
Safety checks are supressed
@ -125,12 +127,14 @@ def _parse_file_silenced(data_file: PathLike) -> Optional[pandas.DataFrame]: @@ -125,12 +127,14 @@ def _parse_file_silenced(data_file: PathLike) -> Optional[pandas.DataFrame]:
pandas data frame with the parsed data or None on error
"""
try:
return parse_file(data_file)
return parse_csv_file(data_file)
except ValueError:
return None
def parse_multiple_files(file_list: Sequence[PathLike]) -> pandas.DataFrame:
def parse_multiple_csv_files(
file_list: Sequence[PathLike],
) -> pandas.DataFrame:
"""parses a list of file paths to one combined data frame
Args:
@ -140,7 +144,7 @@ def parse_multiple_files(file_list: Sequence[PathLike]) -> pandas.DataFrame: @@ -140,7 +144,7 @@ def parse_multiple_files(file_list: Sequence[PathLike]) -> pandas.DataFrame:
"""
if not file_list:
raise ValueError("Empty file list provided")
collection = (_parse_file_silenced(path) for path in file_list)
collection = (_parse_csv_file_silenced(path) for path in file_list)
filtered = (frame for frame in collection if frame is not None)
data_frame = pandas.concat(filtered, ignore_index=True).reset_index()
data_frame[columns.WELL_ROW] = data_frame[columns.WELL_ROW].astype(
@ -191,7 +195,9 @@ def _sanity_check(data_frame: pandas.DataFrame) -> pandas.DataFrame: @@ -191,7 +195,9 @@ def _sanity_check(data_frame: pandas.DataFrame) -> pandas.DataFrame:
return data_frame
def parse_folder(folder: PathLike, quiet: bool = False) -> pandas.DataFrame:
def parse_csv_folder(
folder: PathLike, quiet: bool = False
) -> pandas.DataFrame:
"""parses all csv files in a folder to one large dataframe
Will raise an ValueError, if no sensospot data could be found in
@ -207,7 +213,7 @@ def parse_folder(folder: PathLike, quiet: bool = False) -> pandas.DataFrame: @@ -207,7 +213,7 @@ def parse_folder(folder: PathLike, quiet: bool = False) -> pandas.DataFrame:
folder_path = pathlib.Path(folder)
file_list = find_csv_files(folder_path)
try:
data_frame = parse_multiple_files(file_list)
data_frame = parse_multiple_csv_files(file_list)
except ValueError:
raise ValueError(f"No sensospot data found in folder '{folder}'")

8
tests/conftest.py
Unescape View File

@ -94,16 +94,16 @@ def normalization_data_frame(): @@ -94,16 +94,16 @@ def normalization_data_frame():
@pytest.fixture(scope="session")
def parsed_data_frame_with_params(example_dir):
from sensospot_parser.csv_parser import parse_folder
from sensospot_parser.csv_parser import parse_csv_folder
return parse_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)
return parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)
@pytest.fixture(scope="session")
def parsed_data_frame_without_params(example_dir):
from sensospot_parser.csv_parser import parse_folder
from sensospot_parser.csv_parser import parse_csv_folder
return parse_folder(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS)
return parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS)
@pytest.fixture

46
tests/test_csv_parser.py
Unescape View File

@ -128,9 +128,9 @@ def test_extract_measurement_info_raises_error(filename): @@ -128,9 +128,9 @@ def test_extract_measurement_info_raises_error(filename):
def test_parse_file(example_file):
from sensospot_parser.csv_parser import parse_file
from sensospot_parser.csv_parser import parse_csv_file
result = parse_file(example_file)
result = parse_csv_file(example_file)
columns = {
"Pos.Id",
@ -170,7 +170,7 @@ def test_parse_file(example_file): @@ -170,7 +170,7 @@ def test_parse_file(example_file):
def test_parse_file_raises_error(example_dir):
from sensospot_parser.csv_parser import parse_file
from sensospot_parser.csv_parser import parse_csv_file
csv_file = (
example_dir
@ -179,13 +179,13 @@ def test_parse_file_raises_error(example_dir): @@ -179,13 +179,13 @@ def test_parse_file_raises_error(example_dir):
)
with pytest.raises(ValueError):
parse_file(csv_file)
parse_csv_file(csv_file)
def test_parse_file_silenced_returns_data_frame(example_file):
from sensospot_parser.csv_parser import _parse_file_silenced
from sensospot_parser.csv_parser import _parse_csv_file_silenced
result = _parse_file_silenced(example_file)
result = _parse_csv_file_silenced(example_file)
assert result["Well.Row"][0] == "A"
assert result["Well.Column"][0] == 1
@ -193,7 +193,7 @@ def test_parse_file_silenced_returns_data_frame(example_file): @@ -193,7 +193,7 @@ def test_parse_file_silenced_returns_data_frame(example_file):
def test_parse_file_silenced_returns_none_on_error(example_dir):
from sensospot_parser.csv_parser import _parse_file_silenced
from sensospot_parser.csv_parser import _parse_csv_file_silenced
csv_file = (
example_dir
@ -201,7 +201,7 @@ def test_parse_file_silenced_returns_none_on_error(example_dir): @@ -201,7 +201,7 @@ def test_parse_file_silenced_returns_none_on_error(example_dir):
/ "should_raise_value_error.csv"
)
result = _parse_file_silenced(csv_file)
result = _parse_csv_file_silenced(csv_file)
assert result is None
@ -217,12 +217,12 @@ def test_parse_file_silenced_returns_none_on_error(example_dir): @@ -217,12 +217,12 @@ def test_parse_file_silenced_returns_none_on_error(example_dir):
],
)
def testparse_multiple_files_ok(example_dir, file_list):
from sensospot_parser.csv_parser import parse_multiple_files
from sensospot_parser.csv_parser import parse_multiple_csv_files
sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS
files = [sub_dir / file for file in file_list]
data_frame = parse_multiple_files(files)
data_frame = parse_multiple_csv_files(files)
print(data_frame["Exposure.Id"].unique())
assert len(data_frame) == 100 * len(files)
@ -230,18 +230,18 @@ def testparse_multiple_files_ok(example_dir, file_list): @@ -230,18 +230,18 @@ def testparse_multiple_files_ok(example_dir, file_list):
def testparse_multiple_files_empty_file_list():
from sensospot_parser.csv_parser import parse_multiple_files
from sensospot_parser.csv_parser import parse_multiple_csv_files
with pytest.raises(ValueError):
parse_multiple_files([])
parse_multiple_csv_files([])
def testparse_multiple_files_empty_array(example_dir):
from sensospot_parser.csv_parser import parse_multiple_files
from sensospot_parser.csv_parser import parse_multiple_csv_files
files = [example_dir / "no_array_A1_1.csv"]
data_frame = parse_multiple_files(files)
data_frame = parse_multiple_csv_files(files)
print(data_frame["Exposure.Id"].unique())
assert len(data_frame) == 1
@ -258,9 +258,9 @@ def test_find_csv_files(example_dir): @@ -258,9 +258,9 @@ def test_find_csv_files(example_dir):
def test_parse_folder_no_datetime_records(example_dir):
from sensospot_parser.csv_parser import parse_folder
from sensospot_parser.csv_parser import parse_csv_folder
data_frame = parse_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)
data_frame = parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)
assert len(data_frame) == 36 * 3 * 100
assert len(data_frame["Well.Row"].unique()) == 3
@ -273,7 +273,10 @@ def test_parse_folder_no_datetime_records(example_dir): @@ -273,7 +273,10 @@ def test_parse_folder_no_datetime_records(example_dir):
def test_sanity_check_ok(example_dir):
from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files
from sensospot_parser.csv_parser import (
_sanity_check,
parse_multiple_csv_files,
)
sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS
file_list = [
@ -281,7 +284,7 @@ def test_sanity_check_ok(example_dir): @@ -281,7 +284,7 @@ def test_sanity_check_ok(example_dir):
"160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv",
]
files = [sub_dir / file for file in file_list]
data_frame = parse_multiple_files(files)
data_frame = parse_multiple_csv_files(files)
result = _sanity_check(data_frame)
@ -289,7 +292,10 @@ def test_sanity_check_ok(example_dir): @@ -289,7 +292,10 @@ def test_sanity_check_ok(example_dir):
def test_sanity_check_raises_value_error(example_dir):
from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files
from sensospot_parser.csv_parser import (
_sanity_check,
parse_multiple_csv_files,
)
sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS
file_list = [
@ -297,7 +303,7 @@ def test_sanity_check_raises_value_error(example_dir): @@ -297,7 +303,7 @@ def test_sanity_check_raises_value_error(example_dir):
"160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv",
]
files = [sub_dir / file for file in file_list]
data_frame = parse_multiple_files(files)
data_frame = parse_multiple_csv_files(files)
data_frame = data_frame.drop(data_frame.index[1])
with pytest.raises(ValueError):

4
tests/test_sensospot_data.py
Unescape View File

@ -4,5 +4,5 @@ @@ -4,5 +4,5 @@
def test_import_api():
from sensospot_parser import main # noqa: F401
from sensospot_parser import columns # noqa: F401
from sensospot_parser import parse_file # noqa: F401
from sensospot_parser import parse_folder # noqa: F401
from sensospot_parser import parse_csv_file # noqa: F401
from sensospot_parser import parse_csv_folder # noqa: F401

Write Preview
Loading…
Cancel
Save