diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000000000000000000000000000000000000..dc4c575fe1343ac222be57a9d056e0b766d01183
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1 @@
+exclude lifescale/models/ls_run.py lifescale/scripts/run_gui.py
\ No newline at end of file
diff --git a/README.md b/README.md
index 321815f75c666edd17729d5ffeb67096a1801c7b..4a9f49948138a93a80905cd523c7337386fe5365 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,14 @@
# lifescale_utils
Data analysis tools for lifescale with GUI.
-# Command line programms:
+# Command line programs:
## ls2csv
-The program *ls2csv* reads the content of the xlsm files written by lifescale units, parses the data and writes thems to three csv
-fieles:
- * Masses_Vibrio_[run-name].csv: Contains the data series from the sheet AcquisitionIntervals.
- * SampleMetadata_[run-name].csv: Data from the sheet PanelData.
- * Summary_[run-name].csv: Contains the data from the sheet IntervalAnalysis.
+The program *ls2csv* reads the content of the xlsm files written by lifescale units, parses the data and writes them to three csv
+files (where `[run-name]` is the name from the settings sheet):
+ * `Masses_Vibrio_[run-name].csv`: Data series from the sheet AcquisitionIntervals.
+ * `SampleMetadata_[run-name].csv`: Data from the sheet PanelData.
+ * `Summary_[run-name].csv`: Data from the sheet IntervalAnalysis plus sample related data from AcquisitionIntervals.
### Usage:
* Conversion: `ls2csv -i [path and nale of xlsm file] -o [outpur directory]`
diff --git a/lifescale/__init__.py b/lifescale/__init__.py
index 9e0448d387540c298fffc572385958227863965d..af1d517ca89f1f94b3c97b63573cf5f95052ea4e 100644
--- a/lifescale/__init__.py
+++ b/lifescale/__init__.py
@@ -1,4 +1,4 @@
-"""LifeSclae utils is a utility program for handling data output.
+"""LifeScale utils is a utility program for handling data output.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
@@ -17,8 +17,8 @@ along with this program. If not, see <https://www.gnu.org/licenses/>.
Andreas Hellerschmied (heller182@gmx.at)
"""
-__version__ = '0.0.2'
+__version__ = '0.0.3'
__author__ = 'Andreas Hellerschmied'
__git_repo__ = 'tba'
__email__ = 'heller182@gmx.at'
-__copyright__ = '(c) 2022 Andreas Hellerschmied'
\ No newline at end of file
+__copyright__ = '(c) 2022 Andreas Hellerschmied'
diff --git a/lifescale/command_line/command_line.py b/lifescale/command_line/command_line.py
index 212762d19b1a61cca49eb7db660d71fe6afd0f21..e5c45880ad9d5ce122ab8b9ccf1d125507d2fd1b 100644
--- a/lifescale/command_line/command_line.py
+++ b/lifescale/command_line/command_line.py
@@ -1,4 +1,4 @@
-""" Command line interface of lifescale utils
+"""Command line interface of lifescale utils.
Copyright (C) 2022 Andreas Hellerschmied <heller182@gmx.at>
"""
@@ -25,13 +25,14 @@ def is_dir(pathname):
def ls2csv():
"""Command line interface including argument parser for the lifescale2csv converter."""
parser = argparse.ArgumentParser(prog="ls2csv",
- description="Covnersion from lifescale xlsm output to csv files",
- epilog="The ls2csv converter loads and parses xslm files created by the lifescale "
+ description="Conversion from lifescale xlsm output to csv files",
+ epilog="The ls2csv converter loads and parses xlsm files created by the lifescale "
"unit. It writes several csv files to the output directory that contain "
- "extraced data from the input xlsm file in an easily readable way.",
+ "extracted data from the input xlsm file in an easily readable way.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
- parser.add_argument("-i", "--input-xlsm", type=is_file, required=True, help="Path and name of the input xlsm file created by "
- "lifescale.")
+ parser.add_argument("-i", "--input-xlsm", type=is_file, required=True, help="Path and name of the input xlsm file "
+ "created by "
+ "lifescale.")
parser.add_argument("-o", "--out-dir", type=is_dir, required=True, help="Output directory for the CSV files.")
parser.add_argument("-nv", "--not-verbose", required=False, help="Disable command line status messages.",
action='store_true')
@@ -40,10 +41,8 @@ def ls2csv():
args = parser.parse_args()
verbose = not args.not_verbose
- return ls2csv_main(xlsm_filename=args.input_xlsm, oputput_dir=args.out_dir, verbose=verbose)
+ return ls2csv_main(xlsm_filename=args.input_xlsm, output_dir=args.out_dir, verbose=verbose)
if __name__ == '__main__':
ls2csv()
-
-
diff --git a/lifescale/models/ls_data.py b/lifescale/models/ls_data.py
index 44c70f2a1a9194b0f2755dd284fe1805221a816c..f14a9cdba775f63bd22061a11d6ff6a419dc3299 100644
--- a/lifescale/models/ls_data.py
+++ b/lifescale/models/ls_data.py
@@ -39,18 +39,18 @@ class LSData:
End time of the run.
settings_dict : dict
Contains all settings from the Settings sheet of the input xlsm file. If more than one attributes are provides
- for a parameter (dictionary key), the dictionary item is a list. If no attribute is provided, the item is `None`.
+ for a parameter (dictionary key), the dictionary item is a list. If no attribute is provided, the item is `None`
df_panel_data : pandas dataframe
Pandas dataframe that holds the data of the PanelData sheet of the input xlsm file.
df_interval_analysis : pandas dataframe
Pandas dataframe that holds the data of the IntervalAnalysis sheet plus additional data of the input xlsm file.
df_masses : pandas dataframe
- Pandas dataframe that holds the data derived from the AcquisiotionIntervals sheet of the input xlsm file.
+ Pandas dataframe that holds the data derived from the AcquisitionIntervals sheet of the input xlsm file.
"""
def __init__(self,
run_name='',
- accession_number='',
+ guid='',
input_xlsm_filename='',
output_dir_path='',
start_time_dt=None,
@@ -69,10 +69,10 @@ class LSData:
self.run_name = run_name
else:
raise TypeError('"run_name" needs to be a string')
- if isinstance(accession_number, str):
- self.accession_number = accession_number
+ if isinstance(guid, str):
+ self.guid = guid
else:
- raise TypeError('"accession_number" needs to be a string')
+ raise TypeError('"guid" needs to be a string')
# output_dir_path:
if isinstance(output_dir_path, str):
@@ -123,10 +123,6 @@ class LSData:
# Initialize additional attributes:
pass
-
-
-
-
@classmethod
def from_xlsm_file(cls, input_xlsm_filename, verbose=True):
"""Constructor that generates and populates the LSData object from an xlsm LS output file.
@@ -170,12 +166,12 @@ class LSData:
# Check, if all required sheets are available:
if set(REQUIRED_XLSM_SHEET_NAMES) - set(sheet_names):
- missings_steets = list(set(REQUIRED_XLSM_SHEET_NAMES) - set(sheet_names))
- raise AssertionError(f'The following sheets are missing the file {input_xlsm_filename}: {missings_steets}')
+ missing_sheets = list(set(REQUIRED_XLSM_SHEET_NAMES) - set(sheet_names))
+ raise AssertionError(f'The following sheets are missing the file {input_xlsm_filename}: {missing_sheets}')
# PanelData:
if verbose:
- print(f' - Parse PanalData')
+ print(f' - Parse PanelData')
df_panel_data = xl_file.parse('PanelData')
df_panel_data = remove_space_from_column_names(df_panel_data)
df_panel_data['NumberOfIntervals'] = None
@@ -193,9 +189,11 @@ class LSData:
df_interval_analysis['MeasuredVolume'] = None # From AcquisitionIntervals
df_interval_analysis['ResonantFrequency'] = None # From AcquisitionIntervals
if not (df_interval_analysis[['Id', 'IntervalNumber']].value_counts().count() == len(df_interval_analysis)):
- raise AssertionError(f'The combination if the values in the columns "Id" and "IntervalNumber" in IntervalAnalysis is not unique!')
+ raise AssertionError(
+ f'The combination if the values in the columns "Id" and "IntervalNumber" in IntervalAnalysis is not '
+ f'unique!')
- # Settings:
+ # Settings:
if verbose:
print(f' - Parse Settings')
settings_dict = {}
@@ -213,12 +211,12 @@ class LSData:
else:
settings_dict[row[0]] = tmp_list
run_name = settings_dict['Name']
- if settings_dict['AccessionNumber'] is None:
- accession_number = ''
+ if settings_dict['Guid'] is None:
+ guid = ''
else:
- accession_number = str(settings_dict['AccessionNumber'])
+ guid = str(settings_dict['Guid'])
start_time_dt = settings_dict['StartTime']
- end_time_dt =start_time_dt + dt.timedelta(settings_dict['ElapsedTime']/(24*60))
+ end_time_dt = start_time_dt + dt.timedelta(settings_dict['ElapsedTime'] / (24 * 60))
# # Settings (dataframe):
# df_settings = xl_file.parse('Settings', header=None).transpose()
@@ -226,7 +224,6 @@ class LSData:
# df_settings = df_settings[1:]
# df_settings.reset_index(drop=True, inplace=True)
-
# Masses (from sheet AcquisitionIntervals):
if verbose:
print(f' - Parse Masses')
@@ -240,11 +237,11 @@ class LSData:
transit_time_list = []
pressure_drop_list = []
time_list_length_old = 0
- masses_list_length_old = 0
- volume_list_length_old = 0
- total_num_particles_list_length_old = 0
- transit_time_list_length_old = 0
- pressure_drop_list_length_old = 0
+ # masses_list_length_old = 0
+ # volume_list_length_old = 0
+ # total_num_particles_list_length_old = 0
+ # transit_time_list_length_old = 0
+ # pressure_drop_list_length_old = 0
current_id = None
current_well = None
@@ -256,14 +253,14 @@ class LSData:
if row[0] == 'Id':
current_id = row[1]
if ~(df_interval_analysis['Id'] == current_id).any():
- raise AssertionError(f'"ID="{current_id} is not available in InteralAnalysis!')
+ raise AssertionError(f'"ID="{current_id} is not available in IntervalAnalysis!')
if ~(df_panel_data['Id'] == current_id).any():
raise AssertionError(f'"ID="{current_id} is not available in PanelData!')
continue
if row[0] == 'Well':
current_well = row[1]
if ~(df_interval_analysis['Well'] == current_well).any():
- raise AssertionError(f'"Well="{current_well} is not available in InteralAnalysis!')
+ raise AssertionError(f'"Well="{current_well} is not available in IntervalAnalysis!')
if ~(df_panel_data['Well'] == current_well).any():
raise AssertionError(f'"Well="{current_well} is not available in PanelData!')
continue
@@ -278,7 +275,7 @@ class LSData:
current_interval_num = row[1]
if ~(df_interval_analysis['IntervalNumber'] == current_interval_num).any():
raise AssertionError(
- f'"IntervalNumber="{current_interval_num} is not available in InteralAnalysis!')
+ f'"IntervalNumber="{current_interval_num} is not available in IntervalAnalysis!')
continue
if row[0] == 'StartTime':
continue
@@ -287,37 +284,48 @@ class LSData:
if row[0] == 'DilutionFactor':
continue
if row[0] == 'Status':
- tmp_filter = (df_interval_analysis['Id'] == current_id) & (df_interval_analysis['IntervalNumber'] == current_interval_num)
+ tmp_filter = (df_interval_analysis['Id'] == current_id) & (
+ df_interval_analysis['IntervalNumber'] == current_interval_num)
if len(tmp_filter[tmp_filter]) != 1:
- raise AssertionError(f'Invalid number of matches of "Id={current_id}" and "IntervalNumber={current_interval_num}" in IntervalAnalysis: {len(tmp_filter[tmp_filter])}')
+ raise AssertionError(
+ f'Invalid number of matches of "Id={current_id}" and "IntervalNumber={current_interval_num}" '
+ f'in IntervalAnalysis: {len(tmp_filter[tmp_filter])}')
df_interval_analysis.loc[tmp_filter, 'Status'] = row[1]
continue
if row[0] == 'DetectedParticles':
tmp_filter = (df_interval_analysis['Id'] == current_id) & (
- df_interval_analysis['IntervalNumber'] == current_interval_num)
+ df_interval_analysis['IntervalNumber'] == current_interval_num)
if len(tmp_filter[tmp_filter]) != 1:
- raise AssertionError(f'Invalid number of matches of "Id={current_id}" and "IntervalNumber={current_interval_num}" in IntervalAnalysis: {len(tmp_filter[tmp_filter])}')
+ raise AssertionError(
+ f'Invalid number of matches of "Id={current_id}" and "IntervalNumber={current_interval_num}" '
+ f'in IntervalAnalysis: {len(tmp_filter[tmp_filter])}')
df_interval_analysis.loc[tmp_filter, 'DetectedParticles'] = row[1]
current_detected_particles = row[1] # For cross-checks
continue
if row[0] == 'MeasuredVolume':
tmp_filter = (df_interval_analysis['Id'] == current_id) & (
- df_interval_analysis['IntervalNumber'] == current_interval_num)
+ df_interval_analysis['IntervalNumber'] == current_interval_num)
if len(tmp_filter[tmp_filter]) != 1:
- raise AssertionError(f'Invalid number of matches of "Id={current_id}" and "IntervalNumber={current_interval_num}" in IntervalAnalysis: {len(tmp_filter[tmp_filter])}')
+ raise AssertionError(
+ f'Invalid number of matches of "Id={current_id}" and "IntervalNumber={current_interval_num}" '
+ f'in IntervalAnalysis: {len(tmp_filter[tmp_filter])}')
df_interval_analysis.loc[tmp_filter, 'MeasuredVolume'] = row[1]
continue
if row[0] == 'ResonantFrequency':
tmp_filter = (df_interval_analysis['Id'] == current_id) & (
df_interval_analysis['IntervalNumber'] == current_interval_num)
if len(tmp_filter[tmp_filter]) != 1:
- raise AssertionError(f'Invalid number of matches of "Id={current_id}" and "IntervalNumber={current_interval_num}" in IntervalAnalysis: {len(tmp_filter[tmp_filter])}')
+ raise AssertionError(
+ f'Invalid number of matches of "Id={current_id}" and "IntervalNumber={current_interval_num}" '
+ f'in IntervalAnalysis: {len(tmp_filter[tmp_filter])}')
df_interval_analysis.loc[tmp_filter, 'ResonantFrequency'] = row[1]
continue
if row[0] == 'Time':
tmp_list = row_to_list(row[1:])
if (len(tmp_list) == 0) and (current_detected_particles != 0):
- raise AssertionError(f'Number of "DetectedParticles={current_detected_particles}" does not match length of "Time" series (= {len(tmp_list)}) ')
+ raise AssertionError(
+ f'Number of "DetectedParticles={current_detected_particles}" does not match length of "Time" '
+ f'series (= {len(tmp_list)}) ')
time_list += tmp_list
continue
if row[0] == 'Mass':
@@ -345,7 +353,8 @@ class LSData:
if not (len(time_list) == len(masses_list) == len(volume_list) == len(total_num_particles_list) == len(
transit_time_list) == len(pressure_drop_list)):
raise AssertionError(
- f'The lengths of the data series in AcquisitionIntervals of "Well={current_well}" and "IntervalNumber={current_interval_num}" do not match!')
+ f'The lengths of the data series in AcquisitionIntervals of "Well={current_well}" and '
+ f'"IntervalNumber={current_interval_num}" do not match!')
# Set up lists for well, id and interval number:
num_additional_items_in_data_series = len(time_list) - time_list_length_old
tmp_list = [current_id] * num_additional_items_in_data_series
@@ -356,23 +365,27 @@ class LSData:
interval_num_list += tmp_list
# Reset counters:
time_list_length_old = len(time_list)
- masses_list_length_old = len(masses_list)
- volume_list_length_old = len(volume_list)
- total_num_particles_list_length_old = len(total_num_particles_list)
- transit_time_list_length_old = len(transit_time_list)
- pressure_drop_list_length_old = len(pressure_drop_list)
+ # masses_list_length_old = len(masses_list)
+ # volume_list_length_old = len(volume_list)
+ # total_num_particles_list_length_old = len(total_num_particles_list)
+ # transit_time_list_length_old = len(transit_time_list)
+ # pressure_drop_list_length_old = len(pressure_drop_list)
continue
# Check if the length of all data series lists match:
if not (len(time_list) == len(masses_list) == len(volume_list) == len(total_num_particles_list) == len(
- transit_time_list) == len(pressure_drop_list) == len(id_list) == len(well_list) == len(interval_num_list)):
+ transit_time_list) == len(pressure_drop_list) == len(id_list) == len(well_list) == len(
+ interval_num_list)):
raise AssertionError(
f'The lengths of the data series in AcquisitionIntervals do not match!')
# Create dataframe:
- df_masses_columns = ['Id', 'Well', 'IntervalNumber', 'Time', 'Mass', 'Volume', 'TotalNumberOfParticlesThroughSensor', 'TransitTime', 'PressureDrop']
- df_masses = pd.DataFrame(list(zip(id_list, well_list, interval_num_list, time_list, masses_list, volume_list, total_num_particles_list, transit_time_list, pressure_drop_list)),
- columns = df_masses_columns)
+ df_masses_columns = ['Id', 'Well', 'IntervalNumber', 'Time', 'Mass', 'Volume',
+ 'TotalNumberOfParticlesThroughSensor', 'TransitTime', 'PressureDrop']
+ df_masses = pd.DataFrame(list(
+ zip(id_list, well_list, interval_num_list, time_list, masses_list, volume_list, total_num_particles_list,
+ transit_time_list, pressure_drop_list)),
+ columns=df_masses_columns)
# Sensor:
# sensor_dict = {}
@@ -387,15 +400,15 @@ class LSData:
print(f'...finished loading and parsing data!')
return cls(run_name=run_name,
- accession_number=accession_number,
- input_xlsm_filename=input_xlsm_filename,
- start_time_dt=start_time_dt,
- end_time_dt=end_time_dt,
- settings_dict=settings_dict,
- df_panel_data=df_panel_data,
- df_interval_analysis=df_interval_analysis,
- df_masses=df_masses,
- )
+ guid=guid,
+ input_xlsm_filename=input_xlsm_filename,
+ start_time_dt=start_time_dt,
+ end_time_dt=end_time_dt,
+ settings_dict=settings_dict,
+ df_panel_data=df_panel_data,
+ df_interval_analysis=df_interval_analysis,
+ df_masses=df_masses,
+ )
def export_csv_files(self, output_filepath, verbose=True, sort_by_time=False):
"""Write CSV files to output directory"""
@@ -407,8 +420,8 @@ class LSData:
raise AssertionError(f'The output path does not exist: {output_filepath}')
self.output_dir_path = output_filepath
- if self.accession_number:
- filename_ending = f'{self.run_name}_{self.accession_number}.csv'
+ if self.guid:
+ filename_ending = f'{self.run_name}_{self.guid}.csv'
else:
filename_ending = f'{self.run_name}.csv'
@@ -437,7 +450,7 @@ class LSData:
self.df_interval_analysis.to_csv(filename, index=False)
# TODO: Output format (number of digits)
- # TODO: Select columns for output (setable as parameter + default settings for each csv file)
+ # TODO: Select columns for output (settable as parameter + default settings for each csv file)
# TODO: Optionally order data series by time (parameter)?!
@property
@@ -466,7 +479,8 @@ class LSData:
def __str__(self):
if self.run_name is not None:
- return f'Run "{self.run_name}" with {self.get_number_of_observations} observations in {self.get_number_of_intervals} intervals and {self.get_number_of_wells} wells.'
+ return f'Run "{self.run_name}" with {self.get_number_of_observations} observations in ' \
+ f'{self.get_number_of_intervals} intervals and {self.get_number_of_wells} wells. '
else:
return f'Not data available yet.'
@@ -494,11 +508,9 @@ def row_to_list(row) -> list:
if __name__ == '__main__':
"""Main function, primarily for debugging and testing."""
xlsm_filename = '../../data/Example_several_wells/Vibrio_starvation_24.11.22_221125_163425.xlsm'
- oputput_directory = '../../output/'
+ output_directory = '../../output/'
ls_data = LSData.from_xlsm_file(input_xlsm_filename=xlsm_filename)
- ls_data.export_csv_files(oputput_directory)
+ ls_data.export_csv_files(output_directory)
print('test')
-
-
diff --git a/lifescale/scripts/ls2csv.py b/lifescale/scripts/ls2csv.py
index f13a56795bb5a1e1a748701fa3ef79c42062024c..7903228e2a9711e56e5c173725dfc94016acb436 100644
--- a/lifescale/scripts/ls2csv.py
+++ b/lifescale/scripts/ls2csv.py
@@ -1,11 +1,11 @@
-"""Converstion program from xlsm to csv
+"""Conversion program from xlsm to csv.
Copyright (C) 2022 Andreas Hellerschmied <heller182@gmx.at>"""
from lifescale.models.ls_data import LSData
-def ls2csv(xlsm_filename, oputput_dir, verbose=True):
+def ls2csv(xlsm_filename, output_dir, verbose=True):
"""Convert lifescale output file (xlsm) to csv files."""
ls_data = LSData.from_xlsm_file(input_xlsm_filename=xlsm_filename, verbose=verbose)
- ls_data.export_csv_files(oputput_dir, verbose=verbose)
+ ls_data.export_csv_files(output_dir, verbose=verbose)
diff --git a/lifescale/scripts/run_gui.py b/lifescale/scripts/run_gui.py
index 6d8f018a56a3fae620af93a36f8301e5cc217b24..c7b7fb62509c887fc4a315e287d932242937777f 100644
--- a/lifescale/scripts/run_gui.py
+++ b/lifescale/scripts/run_gui.py
@@ -12,4 +12,4 @@ def run_gui():
if __name__ == "__main__":
"""Main Program."""
- run_gui()
\ No newline at end of file
+ run_gui()
diff --git a/makefile b/makefile
index 54c3aa9b332bea0dfe517994b7cdf84a86f6c8d1..50604b59aac78b45ba9a97620a3214e50df003c5 100644
--- a/makefile
+++ b/makefile
@@ -5,7 +5,7 @@ test:
$(info Test-run for this makefile!)
$(info Yeah!!)
-# Project initaialization
+# Project initialization
init:
pip install -r requirements.txt
@@ -23,6 +23,7 @@ test_pack_uninstall:
# Build package with setuptools (new version):
build:
+ rm -rf lifescale_utils.egg-info/
python -m build
# Upload package to pypi.org
diff --git a/setup.cfg b/setup.cfg
index a82a87c774f2e43f9dbe360234184b299259c59b..5cb308073936bf00b7166d0d1f735ff6878304e2 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -9,6 +9,7 @@ long_description = file: README.md
long_description_content_type = text/markdown
keywords = Lifescale
license = GNU GPLv3
+license_files = LICENSE
classifiers =
License :: OSI Approved :: GNU General Public License (GPL)
Programming Language :: Python :: 3
@@ -26,3 +27,9 @@ install_requires =
[options.entry_points]
console_scripts =
ls2csv = lifescale.command_line.command_line:ls2csv
+
+[options.packages.find]
+exclude =
+ lifescale.gui*
+ lifescale.scripts.run_gui.py
+ lifescale.models.ls_run.py