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jfibsem_dat
Python implementation of the FIBSEM .dat file format developed at Janelia Research Campus, and associated tools. Written for CPython 3.8+.
Based on a reference MATLAB implementation formerly at https://github.com/david-hoffman/FIB-SEM-Aligner (now taken down) and vendorised in ./reference
.
The repo was unmaintained when these copies were made, and so may contain errors (indeed, there are some known inconsistencies).
There is a FIJI implementation here: https://github.com/fiji/IO/blob/master/src/main/java/sc/fiji/io/FIBSEM_Reader.java
This project currently supports v8 of the image specification.
Installation
Basic installation from github:
pip install 'git+https://github.com/clbarnes/jfibsem_dat.git[all]'
This package contains a number of extras:
vis
contains dependencies used for viewing imagesskimage
contains dependencies for downsampling imagesall
contains all of the above
Utilities
datview
usage: datview [-h] [-c CHANNEL] [-C CALIBRATION] [-d DOWNSAMPLE] [-r] file
View a Janelia FIBSEM .dat file. The data can be scaled using the file's
metadata, viewed --raw, or scaled using a --calibration CSV. Uses matplotlib.
positional arguments:
file .dat file to view
optional arguments:
-h, --help show this help message and exit
-c CHANNEL, --channel CHANNEL
Which channel to view (default first). Not all
channels exist.
-C CALIBRATION, --calibration CALIBRATION
CSV file calibrating raw to scaled values
-d DOWNSAMPLE, --downsample DOWNSAMPLE
Downsample the image; good for quicker viewing.
-r, --raw Show raw data rather than scaled electron counts.
dathead
usage: dathead [-h] [-p] [-k KEY] file
Retrieve metadata from the header of a Janelia FIBSEM .dat file, in JSON
format.
positional arguments:
file .dat file to read headers for
optional arguments:
-h, --help show this help message and exit
-p, --pretty Pretty-printing the JSON.
-k KEY, --key KEY Read specific key(s), rather than the whole header. If a
single key is given, just the value is returned (as
JSON); if multiple are given, a JSON object is returned
with keys and values.
dathist
usage: dathist [-h] [-c CHANNEL] [-C CALIBRATION] [-d DOWNSAMPLE] [-r] file
View the histogram of pixel values for one channel of Janelia FIBSEM .dat file
positional arguments:
file .dat file to view
optional arguments:
-h, --help show this help message and exit
-c CHANNEL, --channel CHANNEL
Which channel to view (default first). Not all
channels exist.
-C CALIBRATION, --calibration CALIBRATION
CSV file calibrating raw to scaled values
-d DOWNSAMPLE, --downsample DOWNSAMPLE
Downsample the image; good for quicker viewing.
-r, --raw Show raw data rather than scaled electron counts.
datcalib
usage: datcalib [-h] [-c CHANNEL] [-C CALIBRATION] [-d DOWNSAMPLE] [-r]
[-s SAMPLES] [-V]
file operation [operation ...]
Produce a calibration CSV for some simple exposure corrections
positional arguments:
file .dat file to view
operation Calibration functions to apply. Multiple functions can
be given, and will be applied in order. Given in the
form 'fn_name,kwarg1_name=kwarg1_value,...'. Values
given in JSON format (e.g. 'null' instead of 'None'),
although uncontained strings do not need quoting.
Functions are documented in scikit-image's exposure
package. Accepted functions are: adjust_gamma,
adjust_log, adjust_sigmoid, equalize_hist,
rescale_intensity
optional arguments:
-h, --help show this help message and exit
-c CHANNEL, --channel CHANNEL
Which channel to view (default first). Not all
channels exist.
-C CALIBRATION, --calibration CALIBRATION
CSV file calibrating raw to scaled values
-d DOWNSAMPLE, --downsample DOWNSAMPLE
Downsample the image; good for quicker viewing.
-r, --raw Show raw data rather than scaled electron counts.
-s SAMPLES, --samples SAMPLES
Maximum number of samples in the calibration CSV
-V, --view Whether to show the calibrated result
Format notes
- Field
sw_date
encodes a date as a string of formDD/MM/YYYY
- There are a number of unexplained constants and unanswered questions about the format/ its reference MATLAB implementation: grains of salt are a dependency of using this project.
Contributing
Contributions are welcome!
This project uses black
and isort
for formatting (run make fmt
), and pre-commit
for general code quality checks.
Use make fmt
for formatting and make lint
for spot checks, and pre-commit run --all
to run all hooks.
If you modify any part of the CLI, use make readme
to update the help text in the README.
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