bab5e958cb
NOT WORKING: starts changing the structure of function "deduplicate..."
2026-03-11 15:43:11 +01:00
fc150be724
main now turns content of realtime window analysis into nx dataset
...
the data is not parsed or analysed, it's written as text (well, tsv
technically) - this is only for testing and first attempts
2026-03-11 15:01:04 +01:00
aa3bf531f9
adds example realtime windows analysis
2026-03-11 15:00:15 +01:00
3f97ccee25
removes functions.py
2026-02-17 16:20:08 +01:00
3ae6b86b8e
more elegant solution for deduplicating instruments
...
also edits help for deduplicate_instruments... to better explain what it
does; also fixes small typo ('default=' instead of 'default ='), row 448
2026-02-17 16:15:17 +01:00
d83873c763
raises IndexError if no laser, rheed sys. or chamber is ever specified
...
i.e. if one or more of these fields aren't specified thru all layers
2026-02-17 14:54:33 +01:00
de401b5474
adds instruments metadata to h5 file
2026-02-17 14:39:04 +01:00
fde2615107
changes method of instrument list deduplication
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picks first occurrence in every set (ded_lasers, ded_chambers,
ded_rheeds) and eventually warns user if duplicates exist
2026-02-17 14:37:35 +01:00
59e173c54f
adds rastering and annealing metadata incl. UoM's
2026-02-16 19:40:23 +01:00
712cbc4788
cleans code
2026-02-16 19:40:09 +01:00
207d166227
adds most of the required metadata to function build_nexus_file
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the file is generated into the "output" folder w/ .h5 extension
the most has been done already (probably)
2026-02-16 15:43:07 +01:00
74b8c9cfae
extends pld_fabrication dictionary with UoM's
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now keys with numeric values are sub-dictionaries with a "value" and a
"units" key - unitS not unit to comply directly with NeXus format, which
turned out to be a good idea to avoid confusion since eLabFTW uses the
word "units" for the list of accepted units and "unit" for the selected
one...
NOTE: UoM = Unit of Measurement
2026-02-16 15:39:32 +01:00
1b1834d4e6
some attributes don't default to NoneType anymore
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Target.description defaults to "" (empty str)
Substrate.thickness defaults to "" (empty str)
Substrate.thickness_unit is now hardcoded to "μm"
did you know? apparently h5py does NOT like null values
2026-02-16 15:35:22 +01:00
dfd3c07d2f
ignores h5 and nxs files
2026-02-16 11:50:44 +01:00
d094a60725
replaces elabid with sample name in the names of output files
2026-02-16 11:49:48 +01:00
41ff025098
adds units of measurement (UoM) in Material class and children
2026-02-16 11:30:08 +01:00
ca2cdbfded
adds units of measurement in Layer class
...
plus moves around fullname/operator, created_at and description/body so
that operator is required while the others aren't
2026-02-16 11:28:17 +01:00
b4d7373933
starts working on nexus file creation
2026-02-13 16:23:42 +01:00
2f4985c443
adds h5py to requirements
2026-02-13 16:23:24 +01:00
0a879cbfe9
removes debug line, writes json to file instead (path: output/)
2026-02-13 11:49:59 +01:00
f60b58f2f2
ignores output of main.py (output/*.json)
2026-02-13 11:49:13 +01:00
6f618b2340
adds comments
2026-02-13 01:05:32 +01:00
38940995b5
completes the dataset with instruments_used (in a way...)
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only lacks units of measurement, then I'll be ready for conversion
2026-02-13 00:59:22 +01:00
f686ea65b1
adds get_instruments method to Layer class
...
get_instruments returns a dictionary with the names of every system used
during the deposition
unfortunately, NeXus standard allows for a single value of all three
keys per every sample - not every layer
this means that every layer has its own data for laser, rheed system and
depo chamber which IDEALLY is the same for every layer, but in practice
they COULD be different and I still don't know how to deal with this
2026-02-13 00:32:31 +01:00
23bfdefd30
adds all the remaining layer data
...
only lacks the instrument_used data and units of measurement
NOTE: units of measurement are hard to collect, but could be assumed
considering our instruments are standard
2026-02-13 00:18:07 +01:00
38d281543e
code cleanup: deletes debug lines from main.py
2026-02-13 00:07:39 +01:00
a12506b8be
MAJOR: main.py successfully produces JSON following NeXus-schema
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takes API key and elabid of the "entrypoint" sample as input
returns indented JSON with the reconstructed dataset!
currently lacks instruments_used data (matter of minutes)
and all the layer data (already present in Layer-class objects)
2026-02-13 00:01:24 +01:00
43cfd788f3
adds non-req. attr. "description" to class Target
2026-02-12 23:53:21 +01:00
da42de5466
handles error 400 bad request with exit message
2026-02-12 23:52:37 +01:00
d86b35a5fe
integrates sub-classes Target and Substrate in main.py
2026-02-12 16:01:10 +01:00
c4903a536b
[untested] creates child classes of Material for Substrates and Targets
2026-02-12 15:53:44 +01:00
3e85940eb6
adds chained request from layer to pld target
2026-02-12 15:24:01 +01:00
820337c06e
fixes category title for materials: "Substrate", not "Substrate batch"
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"Substrate" is the title of the category of substrate items
"Substrate batch" is a key in a sample's dictionary
2026-02-12 15:16:35 +01:00
5a605038df
fixes small residual from copy-paste in call_material_from_elabid
...
the fix changes "sample_data" - which was residual from copy-pasting the
call_entrypoint... function and therefore undefined - with
"material_data" which is very well defined in the previous line
2026-02-12 15:09:59 +01:00
fd4c3b718a
creates chain functions to expand the dataset from the entrypoint
2026-02-12 14:58:48 +01:00
7b3bff854d
adds mock layers of mock sample 26015 for testing purposes
2026-02-12 14:37:50 +01:00
4df8048e55
aligns chained requests test with main.py (Layer class)
2026-02-12 14:37:16 +01:00
97d534c5d1
documents main.py functions
2026-02-12 12:15:25 +01:00
88aacf23c1
aligns chained requests test with main.py (debug mode)
2026-02-12 11:29:40 +01:00
43a898e4e6
adds various main.py functions to call entries from elabid's
...
also replaces "pass" with "continue" in loops
2026-02-10 16:15:22 +01:00
5725dbfbf8
adds layer progressive number as Layer class attribute
2026-02-10 15:59:13 +01:00
ddd3775112
http error handling in APIHandler method get_entry_from_elabid()
2026-02-10 15:03:47 +01:00
2117f61f36
changes APIHandler attribute "dump" to "header" for clarity
2026-02-10 15:03:33 +01:00
5aa7527cca
more use(less,ful) comments
2026-02-10 14:46:57 +01:00
c49aa23aea
first attempt to refactor the test code into something more elegant
2026-02-09 17:50:35 +01:00
352a223d95
copies entire Header class in chained_requests test script
2026-02-09 16:53:16 +01:00
1d0bc6668c
moves chained_requests in folder tests
2026-02-09 16:50:59 +01:00
46df7a948f
completes methods for class Material
2026-02-09 16:27:52 +01:00
03d7811904
fixes Layer temperature and pressure keys (deletes trailing whitespace)
...
also changes default elabid to newer resource
2026-02-09 15:14:32 +01:00
c5f85b2618
Layer.__init__: ValueError on num.of pulses is fatal, not warning
...
error message changed accordingly
2026-02-09 15:04:35 +01:00
