Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Usb fs rework #25

Closed
wants to merge 127 commits into from
Closed
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
127 commits
Select commit Hold shift + click to select a range
b0d61db
new example
JacobTh98 Mar 7, 2023
131285b
v=0.4.3
JacobTh98 Mar 7, 2023
04c1841
inserted n_el 16 and 32 save dicts
JacobTh98 Mar 9, 2023
fee4919
updated example scripts
JacobTh98 Mar 10, 2023
4e7ecc9
new example for converting measurement directorys to csv
JacobTh98 Mar 10, 2023
1d0edbb
first implementation of npz to csv
JacobTh98 Mar 10, 2023
90d3b77
corrected plot angle
JacobTh98 Mar 10, 2023
3b4270e
fixed position error of measurement
JacobTh98 Mar 10, 2023
f56fc11
0.4.4
JacobTh98 Mar 10, 2023
badb3c1
added logo
JacobTh98 Mar 10, 2023
b11cbc6
deleted section
JacobTh98 Mar 10, 2023
7b96e55
new release of 0.4.2
JacobTh98 Mar 10, 2023
3fe82b4
added 0.5.0
JacobTh98 Mar 10, 2023
dfce6c7
linting
JacobTh98 Mar 10, 2023
ea75153
Merge branch 'main' into dev
JacobTh98 Mar 10, 2023
a31d210
appended ScioSpecMeasurementConfig
JacobTh98 Mar 10, 2023
af2acba
update examples
JacobTh98 Mar 10, 2023
9b75128
linting
JacobTh98 Mar 10, 2023
b42c409
flake
JacobTh98 Mar 10, 2023
76cafb6
Update README.md
JacobTh98 Mar 11, 2023
f2f7d80
updated docstring and resolved import error
JacobTh98 Mar 13, 2023
5a2cbd6
linting
JacobTh98 Mar 13, 2023
68ab092
deleted old docs
JacobTh98 Mar 13, 2023
670339c
Merge branch 'main' into dev
JacobTh98 Mar 13, 2023
1617cac
added excitation frequency
JacobTh98 Mar 13, 2023
bb6ca18
Inserted exc_freq to dependent files.
JacobTh98 Mar 13, 2023
60fabaf
v==0.5.2
JacobTh98 Mar 13, 2023
024ad4f
prep for pytest publish
JacobTh98 Mar 13, 2023
41191de
pctr
JacobTh98 Mar 13, 2023
00cbdb0
updated picture
JacobTh98 Mar 13, 2023
7b017fb
v==0.6.0
JacobTh98 Mar 13, 2023
498b3de
changed logo
JacobTh98 Mar 13, 2023
d9c99d6
Update README.md
JacobTh98 Mar 13, 2023
2903bc6
Merge branch 'main' into dev
JacobTh98 Mar 13, 2023
2308d6b
v==0.6.1
JacobTh98 Mar 13, 2023
6dad94f
Update README.md
JacobTh98 Mar 13, 2023
bcf5588
angle correction
JacobTh98 Mar 14, 2023
4e44c7e
inserted daytime and temperature
JacobTh98 Mar 16, 2023
b441529
docstring and data format
JacobTh98 Mar 16, 2023
6ae60a9
temperature visualization
JacobTh98 Mar 16, 2023
2b608bb
linting
JacobTh98 Mar 16, 2023
dc4efbf
new visualization and black linting==23.1.0
JacobTh98 Mar 16, 2023
2316b22
updated black==23.1.0
JacobTh98 Mar 16, 2023
722a7a0
pypitest==0.6.1.4
JacobTh98 Mar 17, 2023
8bf7a5e
pypi test == 0.6.1.5
JacobTh98 Mar 17, 2023
1c5242c
pypi test == 0.6.1.5
JacobTh98 Mar 17, 2023
db4b0bb
v==0.6.2
JacobTh98 Mar 23, 2023
660cdda
implemented visualization, not added to init
JacobTh98 Mar 23, 2023
0e44552
linting
JacobTh98 Mar 23, 2023
140670f
linting#2
JacobTh98 Mar 23, 2023
bdcfae0
linting #3
JacobTh98 Mar 23, 2023
fef8390
meshing
JacobTh98 Mar 24, 2023
ea0e6e0
inserted citation cff
JacobTh98 Mar 24, 2023
c89b339
added citation cff
JacobTh98 Mar 24, 2023
19a1f22
Merge branch 'main' into dev
JacobTh98 Mar 24, 2023
c733cc5
zenodo doi
JacobTh98 Mar 24, 2023
1136200
inserted absolute valued potential data
JacobTh98 Mar 24, 2023
81a619b
Implemented mesh generation
JacobTh98 Mar 27, 2023
8f50901
gitignore .vscode
JacobTh98 Mar 27, 2023
42c358f
inserted raw string for fixing error.
JacobTh98 Mar 27, 2023
5060219
changed function names and inserted v computation
JacobTh98 Mar 28, 2023
81692ef
linting
JacobTh98 Mar 28, 2023
758287f
docstring and function descriptions.
JacobTh98 Mar 28, 2023
fe40783
linting
JacobTh98 Mar 28, 2023
687b5c2
skipping first measured value
JacobTh98 Apr 3, 2023
3ffb30a
changed absolute label at potential matrix
JacobTh98 Apr 4, 2023
8e57907
init. mesh for import
JacobTh98 Apr 21, 2023
f54a359
Merge branch 'main' into dev
JacobTh98 Apr 21, 2023
77be2d1
first try to use pyvista
JacobTh98 Apr 25, 2023
1b88ba6
pyvisa changes
JacobTh98 Apr 26, 2023
d3dd55d
changed prepare for ml routine
JacobTh98 Apr 26, 2023
0e35318
Merge branch 'dev' into 3d
JacobTh98 Apr 26, 2023
9a3159b
merge dev to 3d
JacobTh98 Apr 26, 2023
49c1e6c
updated function
JacobTh98 Apr 26, 2023
645356e
Merge branch 'main' into dev
JacobTh98 Apr 26, 2023
6936b97
added file in ignore
JacobTh98 May 15, 2023
35cc1a5
modified configurations and added an example for 32 electrodes measur…
JacobTh98 May 15, 2023
33799fb
modified burst count
JacobTh98 May 15, 2023
82c95a7
deleted prototyping functions.
JacobTh98 May 15, 2023
4111ce6
ignored .vsc settings
JacobTh98 May 15, 2023
e076e71
updated reqs
JacobTh98 May 15, 2023
90edf9c
fixed npz to csv conversion error
JacobTh98 May 16, 2023
fbf8cf6
changed names of example measurements
JacobTh98 May 16, 2023
4ab0e2a
deleted unspecified measurement example.
JacobTh98 May 16, 2023
ef93b59
Adjusting the configurations
JacobTh98 May 16, 2023
5ce9309
Ready for test measurements using 32 electrodes.
JacobTh98 May 16, 2023
f93335e
Inserted Issue marker in npz_to_csv.npz
JacobTh98 May 16, 2023
1109782
working example measurement scripts
JacobTh98 May 17, 2023
b24ffce
updated setup_m
JacobTh98 May 17, 2023
39420a4
linting and ignore
JacobTh98 May 17, 2023
002ec92
linting and updates
JacobTh98 May 17, 2023
be8a970
new example script
JacobTh98 May 17, 2023
b50a64c
pypi test release
JacobTh98 May 17, 2023
2b6c8f6
new release v==0.6.4
JacobTh98 May 17, 2023
a307dd5
Merge branch 'main' into dev
JacobTh98 May 17, 2023
cb0b096
updated readme
JacobTh98 May 22, 2023
0dc60a3
Updated Readme TDB
JacobTh98 May 23, 2023
cb20658
preperations for Ethernet connection
JacobTh98 May 25, 2023
0e52ee3
new pytest version and typos
JacobTh98 Jun 27, 2023
3886535
linting
JacobTh98 Jun 27, 2023
a38f4be
updated and undo some changes from pytest 0.6.4.7
JacobTh98 Jun 28, 2023
edcdda8
release==0.6.4.8
JacobTh98 Jun 28, 2023
705d0b8
channel group repeated bug resolved.
JacobTh98 Jun 28, 2023
9016625
Added further information, optimized the .gitignore.
JacobTh98 Aug 31, 2023
bb91870
fixed current computation configuration bug.
JacobTh98 Aug 31, 2023
7af479f
Merge branch 'main' into dev
JacobTh98 Aug 31, 2023
a2e4f0f
v0.6.5
JacobTh98 Sep 26, 2023
835a4a7
Merge branch 'main' into dev
JacobTh98 Sep 26, 2023
d9cfae1
fixed data type error
JacobTh98 Sep 27, 2023
225b763
enables multiple pattern measurements
JacobTh98 Sep 27, 2023
85caac3
added package function to readme
JacobTh98 Sep 27, 2023
8d01665
typo documentation
JacobTh98 Sep 27, 2023
021f1fe
linting
JacobTh98 Sep 27, 2023
d550f8c
Merge branch 'main' into dev
JacobTh98 Oct 20, 2023
ba05977
Merge branch 'main' into dev
JacobTh98 Nov 17, 2023
919fa5e
SoftwareReset usb-hs
JacobTh98 Nov 21, 2023
03a845f
docstring update
JacobTh98 Nov 21, 2023
066fa84
fixed variable name error
JacobTh98 Nov 21, 2023
4866ce4
updated example
JacobTh98 Aug 30, 2024
78899be
updated custom measurement
JacobTh98 Sep 2, 2024
a7bfc9c
v0.7.1.3 to dev (#24)
JacobTh98 Sep 2, 2024
3744c34
prepared device separation
JacobTh98 Nov 11, 2024
25824dc
expansion of EIT class
JacobTh98 Nov 11, 2024
1ac2104
rework step
JacobTh98 Nov 12, 2024
82a5305
resized graphic
JacobTh98 Nov 12, 2024
c5f3ab6
preapared for new version
JacobTh98 Nov 14, 2024
1c86057
0.8.0
JacobTh98 Nov 14, 2024
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/black.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,4 +11,4 @@ jobs:
with:
options: "--check --diff"
src: "./sciopy"
version: "23.1.0"
version: "24.10.0"
3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
__pycache__/
build/
dist/
.update_package.sh.swp
.eggs/
sciopy.egg-info/
.ipynb_checkpoints
Expand All @@ -18,4 +19,4 @@ examples/npz_to_csv.py
examples/measuremet_16/*
examples/measuremet_32/*
sciopy/eth_*
Driver
Driver
37 changes: 1 addition & 36 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,42 +1,7 @@
# ![sciopy](https://raw.githubusercontent.com/spatialaudio/sciopy/main/doc/images/logo_sciopy.jpg)
<img src="https://raw.githubusercontent.com/spatialaudio/sciopy/main/doc/images/logo_sciopy.jpg" alt="Bildbeschreibung" width="200"/>

This package offers the serial interface for communication with an EIT device from ScioSpec. Commands can be written serially and the system response can be read out. With the current version, it is possible to start and stop measurements with defined burst counts and to read out the measurement data. In addition, the measurement data is packed into a data class for better further processing.

## Install Requirements

All requirements are provided inside the `requirements.txt`. To install them navigate inside the sciopy directory and type:

pip3 install -r requirements.txt # Linux, macOS, Windows
pip install -r requirements.txt # Windows

## Run Example Script

For a single measurement, you can simply run one of the `example` scripts using the command:

python custom_measurement.py

To find the right port you can use:


from sciopy import available_serial_ports
available_serial_ports()

This script establishes a serial connection to the ScioSpec device, sends the measurement configuration, and starts a
measurement. For a successful measurement with 16 electrodes, you have to plug in the 16 electrodes to the port "channel 1-16" at the ScioSpec device. For saving the data, set `save = True` and insert a valid `s_path` to the `scio_spec_measurement_config` at the beginning of the script. If you don't change the path the files will be saved to the current directory.

The example script `prep_data_for_ml.py` can be used for the conversion of a finished measurement.
This script creates a new folder with the ending `_prepared` and puts together the potential values and object positions for all measurements. This could be useful for later application of machine learning.

## Explanation of stored files (.npz)

- `potential matrix` (e.g. variable P) is a 16x16 matrix (n_el=16). If you visualize it using `from sciopy import plot_potential_matrix` you can recognize the used excitation pattern or if an electrode is a defect.
- `p_with_exc` is the matrix P with the excitation electrodes
- `p_without_exc` is the matrix P without the excitation electrodes
- `abs_p_norm_without_ext` is the matrix, normalized between (I think) 0-1 without the excitation electrodes.
- `v_with_ext` is the computed voltage from the potential values containing the excitation electrodes
- `v_without_ext` is the computed voltage from the potential values without the excitation electrodes
- `abs_v_norm_without_ext` is the voltage data, normalized between 0-1 without the excitation electrodes.
- `config` contains some information regarding the measurement procedure.

## Contact

Expand Down
70 changes: 0 additions & 70 deletions examples/custom_measurement.py

This file was deleted.

71 changes: 0 additions & 71 deletions examples/measurement_n_el_16.py

This file was deleted.

71 changes: 0 additions & 71 deletions examples/measurement_n_el_32.py

This file was deleted.

20 changes: 0 additions & 20 deletions examples/prep_npz_data_n_el_16.py

This file was deleted.

59 changes: 0 additions & 59 deletions sciopy/3d_mesh.py

This file was deleted.

Loading
Loading