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sensospot_parser
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xmlparsing
Holger Frey 4 years ago
parent
0ac616648c
commit
be24fbaaca
6 changed files with 30 additions and 27 deletions
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  1. 6
      Makefile
  2. 8
      sensospot_data/normalisation.py
  3. 16
      tests/test_normailsation.py
  4. 4
      tests/test_parameters.py
  5. 21
      tests/test_parser.py
  6. 2
      tests/test_sensovation_data_parser.py

6
Makefile
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@ -51,10 +51,10 @@ clean-test: ## remove test and coverage artifacts
rm -fr htmlcov/ rm -fr htmlcov/
lint: ## reformat with black and check style with flake8 lint: ## reformat with black and check style with flake8
isort -rc sensospot_data isort sensospot_data
isort -rc tests isort tests
black sensospot_data tests black sensospot_data tests
flake8 --ignore E231,W503 sensospot_data tests flake8 --ignore E231,W503,E402 sensospot_data tests
test: ## run tests quickly with the default Python test: ## run tests quickly with the default Python
pytest tests -x --disable-warnings pytest tests -x --disable-warnings

8
sensospot_data/normalisation.py
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@ -24,7 +24,7 @@ def _split_data_frame(data_frame, column):
def _infer_exposure_from_parameters(data_frame): def _infer_exposure_from_parameters(data_frame):
""" infer the exposures from measurement parameters """infer the exposures from measurement parameters
will raise a ValueError if the parameters contain NaNs will raise a ValueError if the parameters contain NaNs
""" """
@ -42,7 +42,7 @@ def _infer_exposure_from_parameters(data_frame):
def apply_exposure_map(data_frame, exposure_map=None): def apply_exposure_map(data_frame, exposure_map=None):
""" applies the parameters of a exposure map to the data frame """applies the parameters of a exposure map to the data frame
exposure map: exposure map:
keys: must be the same as the exposure ids, keys: must be the same as the exposure ids,
@ -124,7 +124,7 @@ def _infer_normalization_map(split_data_frames):
def normalize_exposure_time(split_data_frames): def normalize_exposure_time(split_data_frames):
""" add time normalized values to the split data frames """add time normalized values to the split data frames
The max exposure time per channel is used for normalization. The max exposure time per channel is used for normalization.
""" """
@ -153,7 +153,7 @@ def normalize_measurement(
overflow_column=COL_NAME_SPOT_MEAN, overflow_column=COL_NAME_SPOT_MEAN,
overflow_limit=0.5, overflow_limit=0.5,
): ):
""" augment normalize the measurement exposures """augment normalize the measurement exposures
exposure map: exposure map:
keys: must be the same as the exposure ids, keys: must be the same as the exposure ids,

16
tests/test_normailsation.py
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@ -127,8 +127,8 @@ def test_check_overflow_limit_custom_limit():
def test_reduce_overflow_in_channel(normalization_data_frame): def test_reduce_overflow_in_channel(normalization_data_frame):
from sensospot_data.normalisation import ( from sensospot_data.normalisation import (
_reduce_overflow_in_channel,
_check_overflow_limit, _check_overflow_limit,
_reduce_overflow_in_channel,
) )
data_frame = _check_overflow_limit( data_frame = _check_overflow_limit(
@ -158,8 +158,8 @@ def test_reduce_overflow_in_channel(normalization_data_frame):
def test_reduce_overflow_in_channel_shortcut(normalization_data_frame): def test_reduce_overflow_in_channel_shortcut(normalization_data_frame):
from sensospot_data.normalisation import ( from sensospot_data.normalisation import (
_reduce_overflow_in_channel,
_check_overflow_limit, _check_overflow_limit,
_reduce_overflow_in_channel,
) )
normalization_data_frame["Exposure.Time"] = 1 normalization_data_frame["Exposure.Time"] = 1
@ -201,8 +201,8 @@ def test_reduce_overflow(normalization_data_frame):
def test_infer_normalization_map(normalization_data_frame): def test_infer_normalization_map(normalization_data_frame):
from sensospot_data.normalisation import ( from sensospot_data.normalisation import (
_infer_normalization_map,
_split_data_frame, _split_data_frame,
_infer_normalization_map,
) )
normalization_data_frame.loc[5, "Exposure.Channel"] = "Cy3" normalization_data_frame.loc[5, "Exposure.Channel"] = "Cy3"
@ -216,11 +216,11 @@ def test_infer_normalization_map(normalization_data_frame):
def test_normalize_exposure(normalization_data_frame): def test_normalize_exposure(normalization_data_frame):
from sensospot_data.columns import COLUMN_NORMALIZATION
from sensospot_data.normalisation import ( from sensospot_data.normalisation import (
_normalize_exposure,
reduce_overflow, reduce_overflow,
_normalize_exposure,
) )
from sensospot_data.columns import COLUMN_NORMALIZATION
reduced = reduce_overflow(normalization_data_frame, "Saturation", 1) reduced = reduce_overflow(normalization_data_frame, "Saturation", 1)
result = _normalize_exposure(reduced["Cy5"], 100) result = _normalize_exposure(reduced["Cy5"], 100)
@ -236,8 +236,8 @@ def test_normalize_exposure(normalization_data_frame):
def test_normalize_exposure_time(normalization_data_frame): def test_normalize_exposure_time(normalization_data_frame):
from sensospot_data.normalisation import ( from sensospot_data.normalisation import (
normalize_exposure_time,
reduce_overflow, reduce_overflow,
normalize_exposure_time,
) )
reduced = reduce_overflow(normalization_data_frame, "Saturation", 1) reduced = reduce_overflow(normalization_data_frame, "Saturation", 1)
@ -255,8 +255,8 @@ def test_normalize_exposure_time(normalization_data_frame):
def test_normalize_exposure_time_infered_map(normalization_data_frame): def test_normalize_exposure_time_infered_map(normalization_data_frame):
from sensospot_data.normalisation import ( from sensospot_data.normalisation import (
normalize_exposure_time,
reduce_overflow, reduce_overflow,
normalize_exposure_time,
) )
reduced = reduce_overflow(normalization_data_frame, "Saturation", 1) reduced = reduce_overflow(normalization_data_frame, "Saturation", 1)
@ -273,8 +273,8 @@ def test_normalize_exposure_time_infered_map(normalization_data_frame):
def test_normalize_measurement(example_dir): def test_normalize_measurement(example_dir):
from sensospot_data.normalisation import normalize_measurement
from sensospot_data.parser import process_folder from sensospot_data.parser import process_folder
from sensospot_data.normalisation import normalize_measurement
sub_dir = example_dir / EXAMPLE_DIR_WITH_PARAMS sub_dir = example_dir / EXAMPLE_DIR_WITH_PARAMS
data_frame = process_folder(sub_dir) data_frame = process_folder(sub_dir)

4
tests/test_parameters.py
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@ -34,8 +34,8 @@ def test_ssearch_measurement_params_file_parameters_file(tmpdir):
def test_parse_channel_info(example_dir): def test_parse_channel_info(example_dir):
from sensospot_data.parameters import ( from sensospot_data.parameters import (
_search_measurement_params_file,
_parse_measurement_params, _parse_measurement_params,
_search_measurement_params_file,
) )
params = _search_measurement_params_file( params = _search_measurement_params_file(
@ -70,8 +70,8 @@ def test_get_measurement_params_file_not_found(example_dir):
def test_add_measurement_params(exposure_df): def test_add_measurement_params(exposure_df):
from sensospot_data.parameters import ( from sensospot_data.parameters import (
_add_measurement_params,
MeasurementParams, MeasurementParams,
_add_measurement_params,
) )
params = { params = {

21
tests/test_parser.py
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@ -68,9 +68,10 @@ def test_parse_csv_no_array(example_dir):
"input, expected", [("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")] "input, expected", [("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")]
) )
def test_guess_decimal_separator_returns_correct_separator(input, expected): def test_guess_decimal_separator_returns_correct_separator(input, expected):
from sensospot_data.parser import _guess_decimal_separator
from io import StringIO from io import StringIO
from sensospot_data.parser import _guess_decimal_separator
handle = StringIO(f"header\n{input}\n") handle = StringIO(f"header\n{input}\n")
result = _guess_decimal_separator(handle) result = _guess_decimal_separator(handle)
@ -78,9 +79,10 @@ def test_guess_decimal_separator_returns_correct_separator(input, expected):
def test_guess_decimal_separator_rewinds_handle(): def test_guess_decimal_separator_rewinds_handle():
from sensospot_data.parser import _guess_decimal_separator
from io import StringIO from io import StringIO
from sensospot_data.parser import _guess_decimal_separator
handle = StringIO("\n".join(["header", "data_line"])) handle = StringIO("\n".join(["header", "data_line"]))
_guess_decimal_separator(handle) _guess_decimal_separator(handle)
@ -126,9 +128,10 @@ def test_extract_measurement_info_raises_error(filename):
def test_cleanup_data_columns(): def test_cleanup_data_columns():
from sensospot_data.parser import _cleanup_data_columns
from pandas import DataFrame from pandas import DataFrame
from sensospot_data.parser import _cleanup_data_columns
columns = ["Rect.", "Contour", " ID ", "Found", "Dia."] columns = ["Rect.", "Contour", " ID ", "Found", "Dia."]
data = {col: [i] for i, col in enumerate(columns)} data = {col: [i] for i, col in enumerate(columns)}
data_frame = DataFrame(data=data) data_frame = DataFrame(data=data)
@ -274,8 +277,8 @@ def test_sanity_check_raises_value_error(example_dir):
def test_get_cache_table_name(): def test_get_cache_table_name():
from sensospot_data.parser import _get_cache_table_name
from sensospot_data import VERSION_TABLE_NAME from sensospot_data import VERSION_TABLE_NAME
from sensospot_data.parser import _get_cache_table_name
result = _get_cache_table_name() result = _get_cache_table_name()
@ -283,7 +286,7 @@ def test_get_cache_table_name():
def test_process_folder_creates_cache(dir_for_caching): def test_process_folder_creates_cache(dir_for_caching):
from sensospot_data.parser import process_folder, CACHE_FILE_NAME from sensospot_data.parser import CACHE_FILE_NAME, process_folder
cache_path = dir_for_caching / CACHE_FILE_NAME cache_path = dir_for_caching / CACHE_FILE_NAME
assert not cache_path.is_file() assert not cache_path.is_file()
@ -309,7 +312,7 @@ def test_process_folder_reads_from_cache(dir_for_caching, example_file):
def test_process_folder_read_cache_fails_silently( def test_process_folder_read_cache_fails_silently(
dir_for_caching, exposure_df dir_for_caching, exposure_df
): ):
from sensospot_data.parser import process_folder, CACHE_FILE_NAME from sensospot_data.parser import CACHE_FILE_NAME, process_folder
cache_path = dir_for_caching / CACHE_FILE_NAME cache_path = dir_for_caching / CACHE_FILE_NAME
exposure_df.to_hdf(cache_path, "unknown table") exposure_df.to_hdf(cache_path, "unknown table")
@ -321,9 +324,9 @@ def test_process_folder_read_cache_fails_silently(
def test_process_folder_read_cache_no_cache_arg(dir_for_caching, exposure_df): def test_process_folder_read_cache_no_cache_arg(dir_for_caching, exposure_df):
from sensospot_data.parser import ( from sensospot_data.parser import (
CACHE_FILE_NAME,
process_folder, process_folder,
_get_cache_table_name, _get_cache_table_name,
CACHE_FILE_NAME,
) )
cache_path = dir_for_caching / CACHE_FILE_NAME cache_path = dir_for_caching / CACHE_FILE_NAME
@ -335,7 +338,7 @@ def test_process_folder_read_cache_no_cache_arg(dir_for_caching, exposure_df):
def test_process_folder_writes_cache(dir_for_caching): def test_process_folder_writes_cache(dir_for_caching):
from sensospot_data.parser import process_folder, CACHE_FILE_NAME from sensospot_data.parser import CACHE_FILE_NAME, process_folder
process_folder(dir_for_caching, use_cache=True) process_folder(dir_for_caching, use_cache=True)
@ -344,7 +347,7 @@ def test_process_folder_writes_cache(dir_for_caching):
def test_process_folder_writes_cache_no_cache_arg(dir_for_caching): def test_process_folder_writes_cache_no_cache_arg(dir_for_caching):
from sensospot_data.parser import process_folder, CACHE_FILE_NAME from sensospot_data.parser import CACHE_FILE_NAME, process_folder
process_folder(dir_for_caching, use_cache=False) process_folder(dir_for_caching, use_cache=False)

2
tests/test_sensovation_data_parser.py
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@ -5,6 +5,6 @@ def test_import_api():
from sensospot_data import CACHE_FILE_NAME # noqa: F401 from sensospot_data import CACHE_FILE_NAME # noqa: F401
from sensospot_data import parse_file # noqa: F401 from sensospot_data import parse_file # noqa: F401
from sensospot_data import parse_folder # noqa: F401 from sensospot_data import parse_folder # noqa: F401
from sensospot_data import parse_multiple_files # noqa: F401
from sensospot_data import process_folder # noqa: F401 from sensospot_data import process_folder # noqa: F401
from sensospot_data import parse_multiple_files # noqa: F401
from sensospot_data import normalize_measurement # noqa: F401 from sensospot_data import normalize_measurement # noqa: F401

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