Commit Graph

102 Commits

Author SHA256 Message Date
45220bbaf3 docs finished up to usage, ignores drawio bkp 2026-05-14 17:08:56 +02:00
dc916b1207 new docs, up to installation procedure 2026-05-14 01:40:54 +02:00
50a1ba9f22 first docfiles (asciidoc) - not completed
not even the introduction is full
2026-05-13 21:01:05 +02:00
8962135f0e adds example .env file 2026-05-13 12:38:00 +02:00
ee96100a73 uses dotenv to store api key and other important variables
if a value is not found in .env it will be prompted, but not checked
next step is user docs
2026-05-13 12:31:26 +02:00
686f869d10 documents all the functions/classes/methods (by hand)
no AI used, it took more than I'm willing to admit but it's done
2026-05-13 12:12:32 +02:00
2eea3fc2dd ignores output/attachments 2026-05-13 10:27:40 +02:00
cbf5cdd115 clears comments 2026-05-13 10:26:15 +02:00
a6d4c72f9c adds dependency: dotenv 2026-05-13 09:53:57 +02:00
7e808509cc THIS should solve the naming problem
new class for the Proposals, only outputs their names
if name contains "Proposal ", that gets cropped out
if no proposal is specified the name of the sample shall not include one
2026-05-12 22:59:19 +02:00
2bbab96ca7 rm unnecessary fstring 2026-05-12 16:48:04 +02:00
f84478a7a4 this should solve the filename problem 2026-05-12 16:08:49 +02:00
19a802694f MAJOR: fundamental functions of the parser are ready and tested!
TO-DO:
1. follow the "TO-DO" comments to clean the code
2. filename should be NFFA-DI compliant like:
	nffa-di_NA01_Napoli_Na-26-015.h5
3. rheed data analysis should take two distinct functions
   one for the raw stream and one for the image
4. if time allows: consider moving most of main.py in separate modules
2026-05-12 15:38:06 +02:00
df927b7c0e Layer class methods to list attachments up and tested 2026-05-12 13:51:59 +02:00
ccf74fca26 methods to download experiments attachments up and tested
to-do: clean code
2026-05-12 13:36:52 +02:00
07aac3e6b3 unfinished work 2026-05-12 12:54:16 +02:00
c5b17bb3f8 minimal modifications v0.1.0 2026-05-09 00:15:52 +02:00
865f5cab6b untested: adds methods to Layer class to fetch attachments list
one method fetches all
one filters textual uploads
one filters png and bmp images
2026-05-08 23:40:14 +02:00
0102bb282e improves documentation, tabbing and error handling in APIHandler class
Claude Code helped with autocompletion, the rest is my work
2026-05-08 23:31:36 +02:00
1ef944288e creates APIHandler methods for downloading attachments
method 'download_attachments_data" works with elabapi.UploadsApi() class
to download binary data and other metadata of our files.
CURRENTLY it downloads every single attachment which is not intended
and it's only for testing purposes

"download_attachments_to_disk" saves binary data to "output/attachments"
2026-05-08 18:11:53 +02:00
8e7a424320 adds new bmp RHEED picture for testing 2026-05-08 18:10:15 +02:00
008bcff826 LazyVim tab fix + new unused Layer-class methods to fetch uploads 2026-05-08 18:09:03 +02:00
51b8ea7dd7 adds elabapi_python to requirements 2026-05-08 17:52:32 +02:00
8c616dee2c adds a randomly generated RWA
RWA_Noise has 4 columns: time and 3 intensities.
the RWA is generated through python-random starting from the original
RWA, so that every value is its corresponent in the original file times
a random float number bw/ .8 and 1.2 (noise)
2026-05-08 15:27:45 +02:00
bb1ea8f1c3 proposed: schemas are placed in src/schema (module)
separating schemas from main.py might be a good idea since the parser
will support more fabrication methods, but since every method has its
dictionary is it even possible?
2026-05-08 11:20:10 +02:00
207de511fa transposes rheed intensities, adds shebang to main.py 2026-05-08 10:05:47 +02:00
aa5c114b3b matrix no more normalized 2026-05-05 12:15:57 +02:00
b26433d7ec test image 2026-05-05 12:15:45 +02:00
7a871a9f6d adds useless attrs suggested by DeepSeek
leaving this here as a memento that LLM's allucinate
2026-05-05 12:11:27 +02:00
a278119be4 diffraction image successfully loaded in nexus file 2026-05-05 12:02:39 +02:00
707ce28156 lazy vim auto clean + starting point for image analysis 2026-05-05 11:40:57 +02:00
173ae24aa8 adds pillow (PIL) to requirements for image processing 2026-04-27 15:23:18 +02:00
1d8fd5af15 handles absence of laser energy value 2026-04-27 15:09:52 +02:00
038f1920ba error message includes missing item case 2026-04-24 10:37:10 +02:00
1523c973f4 another attempt at parsing RWA - seems to work better 2026-03-20 15:02:12 +01:00
5cf67648af adds mod. suggested by ClaudeAI - still doesn't work
original code is commented below, rows 517-545
2026-03-18 15:15:31 +01:00
839799a13f adds new function to analyze rheed data, doesn't really work atm
thanks DeepSeek
2026-03-16 12:51:05 +01:00
10c68bf260 reworks how instruments are recorded in the nx file according to new ver
the instruments_used group is still present outside the multilayer group
but currently a new instruments_used sub-group is created in the
layer-specific group

instruments used to deposit a single layer are in
/sample/multilayer/layer_N/instruments_used and there's only one value
for each category (rheed, laser, chamber)
in /instruments_used (root) for each category there's a list of every
(unique) instrument involved in the full deposition process
2026-03-13 15:11:53 +01:00
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
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
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
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