Holger Frey
1513a94a87
Comparing xml to csv parsing results now also checks that the columns are identical
2 years ago
Holger Frey
8169daeb89
Added parser for the assay results xml file
...
The `sensospot_parser.parse_folder()` function now tries to parse the xml file first and will fall back to parsing csv files if an error occurs
2 years ago
Holger Frey
988c7562d9
renamed some functions in "csv_parser" module to have more explicit names
2 years ago
Holger Frey
8644a25d78
moved _cleanup_data_columns() function to "columns" module
...
by moving this function it can be easily reused in the upcoming "xml_parser" module
2 years ago
Holger Frey
99d0e0fa4e
renamed test cases and added a new one for xml parsing
2 years ago
Holger Frey
938b063069
removed the "recordtime" module
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The "recordtime" module uses the assay result xml file for retrieving the Analyses.Datetime value.
This value is only available in the assay result xml.
Since the "parse_csv" module will only be a backup if this xml file is not present, a separate parser for the Analysis.Datetime is not needed anymore
2 years ago
Holger Frey
873091504c
renamed the "parser" module to "csv_parser"
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The "csv_parser" module will be used as a backup if the analysis xml file is not present.
2 years ago
Holger Frey
78c5db031a
Added image name and recording datetime to the results
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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
2 years ago
Holger Frey
fde3513809
renamed package to 'sensospot_parser'
3 years ago
Holger Frey
4c69ef457b
added type hints and more docs to parser
3 years ago
Holger Frey
81db693157
added typing information to module parameters
3 years ago
Holger Frey
64cee96485
simplified adding parsed parameters
3 years ago
Holger Frey
b86971cd5a
made the api import test nicer
3 years ago
Holger Frey
04b2c8b598
renamed test for package api
3 years ago
Holger Frey
38224770ad
renamed column constants
3 years ago
Holger Frey
c03cff6ad4
added option to recurse one level down
3 years ago
Holger Frey
75ac4740a5
fixed sanity check
3 years ago
Holger Frey
0290c0a9ba
removed "utils" and "dynamic_range"
...
this two modules should be added to a new project. This project should concentrate on on just parsing the data.
3 years ago
Holger Frey
994a06a8f3
added more tests for apply_map()
3 years ago
Holger Frey
791bc51deb
linted
3 years ago
Holger Frey
9359cc00af
added api function apply_map
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this also lead to simplifications in _add_measurement_params and apply_exposure_map
3 years ago
Holger Frey
71ad6c7977
bumped version
3 years ago
Holger Frey
2274a2101b
changed defaults for xdr since sensospot bug is fixed
3 years ago
Holger Frey
dc8851d40e
removed aggregate utils, they don't belong in this library
3 years ago
Holger Frey
dc8e7d5273
changed 'split_data_frame' to 'split'
4 years ago
Holger Frey
d6dac702e7
normalize_values() will respect preset exposure time
4 years ago
Holger Frey
6a00ac943d
added aggregation utility methods
4 years ago
Holger Frey
2ad90af448
removed get_meaurement_params from public api
4 years ago
Holger Frey
4a3cecbe7b
removed module 'normalisation' in favor of 'dynamic_range'
4 years ago
Holger Frey
9eb2396b82
added checks for exposure map validity
4 years ago
Holger Frey
fa94fbc6a5
added silenced parsing of data files
4 years ago
Holger Frey
89c04e9b93
moved exposure maps out of normalization module
4 years ago
Holger Frey
9e485277b6
fixed typo in filename
4 years ago
Holger Frey
67393144c6
added new submodule 'utils'
4 years ago
Holger Frey
8d16635b46
renamed test for __init__.py
4 years ago
Holger Frey
ee6d7ff750
normalization is working prior to refactoring
4 years ago
Holger Frey
e641c341f8
tests passing after cleanup
4 years ago
Holger Frey
8643219e32
removed normalization module, will be rewritten
4 years ago
Holger Frey
b264f1c904
some errors fixed in production
4 years ago
Holger Frey
58d49bf967
api changes
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- normilization api for measurement changed to
`split_channels`
- named tuple for exposure maps exposed in package as
`ExposureInfo`
4 years ago
Holger Frey
809382a2b2
normilization api for single channels has changed
4 years ago
Holger Frey
be24fbaaca
linted
4 years ago
Holger Frey
0ac616648c
remove custom normalization map
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normilization of exposure time is always to the largest time available
4 years ago
9acf7d9c0a
added measurement normalization
4 years ago
e7c56a1f3a
measurement parameters are parsed again
4 years ago
8b782f75ff
removed params info parsing
4 years ago
ec1d7bd8f3
renamed project
5 years ago
ef00e80700
moved main code into .parser submodule
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this should lead to a cleaner structur when a cli module is added.
Also the public facing methods are now clearly defined.
5 years ago
3c20598927
working parser, cli missing
5 years ago
fabbbe3621
parsing of CSV data files
5 years ago
Holger Frey