Dev (#17)

* new example

* v=0.4.3

* inserted n_el 16 and 32 save dicts

* updated example scripts

* new example for converting measurement directorys to csv

* first implementation of npz to csv

* corrected plot angle

* fixed position error of measurement

* 0.4.4

* added logo

* deleted section

* new release of 0.4.2

* added 0.5.0

* linting

* appended ScioSpecMeasurementConfig

* update examples

* linting

* flake

* Update README.md

* updated docstring and resolved import error

* linting

* deleted old docs

* added excitation frequency

* Inserted exc_freq to dependent files.

* v==0.5.2

* prep for pytest publish

* pctr

* updated picture

* v==0.6.0

* changed logo

* Update README.md

* v==0.6.1

* Update README.md

* angle correction

* inserted daytime and temperature

* docstring and data format

* temperature visualization

* linting

* new visualization and black linting==23.1.0

* updated black==23.1.0

* pypitest==0.6.1.4

* pypi test == 0.6.1.5

* pypi test == 0.6.1.5

* v==0.6.2

* implemented visualization, not added to init

* linting

* linting#2

* linting #3

* meshing

* inserted citation cff

* added citation cff

* zenodo doi

* inserted absolute valued potential data

* Implemented mesh generation

* gitignore .vscode

* inserted raw string for fixing error.

* changed function names and inserted v computation

* linting

* docstring and function descriptions.

* linting

* skipping first measured value

* changed absolute label at potential matrix

* init. mesh for import

* first try to use pyvista

* pyvisa changes

* changed prepare for ml routine

* merge dev to 3d

* updated function

* added file in ignore

* modified configurations and added an example for 32 electrodes measurement

* modified burst count

* deleted prototyping functions.

* ignored .vsc settings

* updated reqs

* fixed npz to csv conversion error

* changed names of example measurements

* deleted unspecified measurement example.

* Adjusting the configurations

* Ready for test measurements using 32 electrodes.

* Inserted Issue marker in npz_to_csv.npz

* working example measurement scripts

* updated setup_m

* linting and ignore

* linting and updates

* new example script

* pypi test release

* new release v==0.6.4

* updated readme

* Updated Readme TDB

* preperations for Ethernet connection

* new pytest version and typos

* linting

* updated and undo some changes from pytest 0.6.4.7

* release==0.6.4.8

* channel group repeated bug resolved.

* Added further information, optimized the .gitignore.

* fixed current computation configuration bug.

* v0.6.5

Author: JacobTh98

README.md

@@ -11,19 +11,24 @@ All requirements are provided inside the `requirements.txt`. To install them nav
 
 ## Run Example Script
 
-For a single measurement, you can simply run the `example` scripts using the command:
+For a single measurement, you can simply run one of the `example` scripts using the command:
 
-    python measurement_n_el_16.py
+    python custom_measurement.py
+
+To fing 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 with a burst count of 10. For a successful measurement, 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.
+measurement. For a successful measurement with 16 electordes, 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 second provided example script `prep_data_for_ml.py` can be used for the conversion of a finished measurement.
+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
@@ -35,14 +40,17 @@ This script creates a new folder with the ending `_prepared` and puts together t
 
 ## TBD
 
-- [ ] Communication using LAN connection.
-- [ ] Measurements using 48, 64 electrodes.
-- [ ] Adjacent and opposite injection pattern combination.
+- [x] Measurements using up to 64 electrodes.
+- [x] Measurements using the USB-HS port (Windows).
+- [x] Adjacent and opposite injection pattern combination.
 - [x] Measurements using 32 electrodes.
 - [x] Parsing measurements of 32 electrodes.
 - [x] Adjacent and opposite drive patterns for 32 electrodes.
 - [x] Measurement using 16 electrodes in opposite and adjacent injection pattern.
+- [ ] Communication using LAN connection.
 
 ## Contact
 
+If you have ideas or other advises don't hesitate to contact me!
+
 Email: jacob.thoenes@uni-rostock.de

examples/custom_measurement.py

@@ -17,17 +17,22 @@
 files_offset = 0
 
 sciospec_measurement_setup = ScioSpecMeasurementSetup(
-    burst_count=1,
-    total_meas_num=10,
-    n_el=16,
-    channel_group=[1],
+    burst_count=1,  # The number of measurements to be performed.
+    total_meas_num=10,  # Repetitions of burst count
+    n_el=64,  # Set 16, 32, 48 or 64 and do not forget to change the channel_group.
+    channel_group=[
+        1,
+        2,
+        3,
+        4,
+    ],  # Use [1] for n_el=16, [1,2] for n_el=32, [1,2,3] for n_el=48, and [1,2,3,4] for n_el=64
     exc_freq=10_000,  # 10,000Hz = 10kHz
-    framerate=5,
+    framerate=5,  # Measurements per second
     amplitude=0.01,  # 0.01A = 10mA (maximum)
-    inj_skip=0,
+    inj_skip=0,  # injection electrode skip
     gain=1,
     adc_range=1,  # +/- 1V
-    notes="None",
+    notes="None",  # add measurement information
     configured=False,
 )
 

sciopy/setup_m.py

@@ -538,6 +538,28 @@ def reshape_full_message_in_bursts(
     - delete acknowledgement message: lst.shape=(4480,0) | lst.shape=(89600,)
     - split this depending on burst count: split_list.shape=(5, 8960) | split_list.shape=(5, 17920)
     """
+
+    def length_correction(array: list) -> list:
+        """
+        Implemented by: Oveys Javanmardtilaki
+        """
+        seq_index = 0
+        mask = np.ones(len(array), dtype=bool)
+        seq_to_remove = ["18", "1", "92", "18"]
+        for i in range(len(array)):
+            if seq_to_remove[seq_index] in array[i]:
+                seq_index += 1
+                if seq_index == len(seq_to_remove):
+                    start = i - len(seq_to_remove) + 1
+                    end = i + 1
+                    mask[start:end] = False
+                    seq_index = 0
+            else:
+                seq_index = 0
+        new_array = array[mask]
+        return new_array
+
+    lst = length_correction(lst)
     split_list = []
     # delete acknowledgement message
     lst = lst[4:]

setup.py

@@ -2,7 +2,7 @@
 
 setuptools.setup(
     name="sciopy",
-    version="0.6.4.9",
+    version="0.6.5.0",
     author="Jacob Peter Thönes",
     author_email="jacob.thoenes@uni-rostock.de",
     description="Python based interface module for communication with the ScioSpec Electrical Impedance Tomography (EIT) device.",