Dev (#23)

* 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

* fixed data type error

* enables multiple pattern measurements

* added package function to readme

* typo documentation

* linting

* SoftwareReset usb-hs

* docstring update

* fixed variable name error

* updated example

Author: JacobTh98

examples/custom_measurement.py

@@ -2,69 +2,47 @@
 
 from sciopy import (
     SystemMessageCallback,
-    set_measurement_config,
-    connect_COM_port,
-    StartStopMeasurement,
-    reshape_full_message_in_bursts,
-    del_hex_in_list,
-    split_bursts_in_frames,
+    sciospec_measurement,
+    connect_COM_port_usb_hs,
+    set_measurement_config_usb_hs,
+    SystemMessageCallback_usb_hs,
 )
 
 from sciopy.sciopy_dataclasses import ScioSpecMeasurementSetup
 
 s_path = ""
-files_offset = 0
 
-sciospec_measurement_setup = ScioSpecMeasurementSetup(
+Sciospec = connect_COM_port_usb_hs()
+
+ssms = ScioSpecMeasurementSetup(
     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.
+    total_meas_num=1,  # Repetitions of burst count
+    n_el=32,  # 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,  # Measurements per second
+    exc_freq=125_000,  # 10,000Hz = 10kHz
+    framerate=10,  # Measurements per second
     amplitude=0.01,  # 0.01A = 10mA (maximum)
-    inj_skip=0,  # injection electrode skip
+    inj_skip=16,  # injection electrode skip
     gain=1,
     adc_range=1,  # +/- 1V
-    notes="None",  # add measurement information
-    configured=False,
+    notes="test measurement",  # add measurement information
+    configured=True,
 )
 
-# Connect ScioSpec device
-COM_ScioSpec = connect_COM_port(port="/dev/ttyACM0")
-
-# Send configuration
-set_measurement_config(serial=COM_ScioSpec, ssms=sciospec_measurement_setup)
-
-# Read out system callback
-SystemMessageCallback(COM_ScioSpec, prnt_msg=True)
-
-# Start and stop single measurement
-measurement_data_hex = StartStopMeasurement(COM_ScioSpec)
-# Delete hex in mesured buffer
-measurement_data = del_hex_in_list(measurement_data_hex)
-# Reshape the full mesaurement buffer. Depending on number of electrodes
-split_measurement_data = reshape_full_message_in_bursts(
-    measurement_data, sciospec_measurement_setup
-)
-measurement_data = split_bursts_in_frames(
-    split_measurement_data, sciospec_measurement_setup
-)
+set_measurement_config_usb_hs(Sciospec, ssms)
+SystemMessageCallback_usb_hs(Sciospec, prnt_msg=True)
 
-# Set to "True" to save single measurement
-save = True
+sciospec_data = sciospec_measurement(Sciospec, ssms)
 
-if save:
-    for bursts in measurement_data:
-        np.savez(
-            s_path + "sample_{0:06d}.npz".format(files_offset),
-            config=sciospec_measurement_setup,
-            data=bursts,
-        )
-        files_offset += 1
-    SystemMessageCallback(COM_ScioSpec, prnt_msg=False)
+file_idx = 0
+for bursts in sciospec_data:
+    np.savez(
+        s_path + "sample_{0:06d}.npz".format(file_idx),
+        config=ssms,
+        data=bursts,
+    )
+    file_idx += 1
+SystemMessageCallback(COM_ScioSpec, prnt_msg=False)

examples/measurement_n_el_16.py

@@ -8,6 +8,7 @@
     convert_fulldir_doteit_to_npz,
 )
 
+
 from .com_handling import (
     available_serial_ports,
     connect_COM_port,
@@ -20,6 +21,7 @@
     set_measurement_config_usb_hs,
     SystemMessageCallback_usb_hs,
     StartStopMeasurement_usb_hs,
+    SoftwareReset_usb_hs,
 )
 
 from .print_command_info import (
@@ -102,6 +104,8 @@
     mesh_sample,
 )
 
+from .sciospec_hs import sciospec_measurement
+
 # TBD from .configurations import configuration_01
 
 __all__ = [
@@ -123,6 +127,7 @@
     "set_measurement_config_usb_hs",
     "SystemMessageCallback_usb_hs",
     "StartStopMeasurement_usb_hs",
+    "SoftwareReset_usb_hs",
     # .print_command_info
     "print_syntax",
     "print_general_system_messages",
@@ -190,4 +195,6 @@
     "add_circle_anomaly",
     "plot_mesh",
     "mesh_sample",
+    # .sciospec_hs
+    "sciospec_measurement",
 ]

examples/measurement_n_el_32.py

@@ -0,0 +1,21 @@
+try:
+    import serial
+except ImportError:
+    print("Could not import module: serial")
+
+from sciopy import (
+    StartStopMeasurement_usb_hs,
+    del_hex_in_list,
+    reshape_full_message_in_bursts,
+    split_bursts_in_frames,
+)
+
+from sciopy.sciopy_dataclasses import ScioSpecMeasurementSetup
+
+
+def sciospec_measurement(COM_Sciospec, ssms: ScioSpecMeasurementSetup) -> None:
+    measurement_data_hex = StartStopMeasurement_usb_hs(COM_Sciospec)
+    measurement_data = del_hex_in_list(measurement_data_hex)
+    split_measurement_data = reshape_full_message_in_bursts(measurement_data, ssms)
+    measurement_data = split_bursts_in_frames(split_measurement_data, ssms)
+    return measurement_data

sciopy/__init__.py

@@ -1,5 +1,6 @@
 from pyftdi.ftdi import Ftdi
 import struct
+import time
 from typing import Union
 from sciopy.sciopy_dataclasses import (
     ScioSpecMeasurementSetup,
@@ -266,3 +267,19 @@ def StartStopMeasurement_usb_hs(serial: Ftdi, print_msg: bool = False) -> list:
     serial.write_data(bytearray([0xB4, 0x01, 0x00, 0xB4]))
     SystemMessageCallback_usb_hs(serial, prnt_msg=False, ret_hex_int="int")
     return measurement_data_hex
+
+
+def SoftwareReset_usb_hs(serial: Ftdi, print_msg: bool = True) -> None:
+    """
+    Reset the ScioSpec device.
+
+    Parameters
+    ----------
+    serial : Ftdi
+        USB-HS serial connection
+    print_msg : bool, optional
+        print the callback message, by default True
+    """
+    serial.write_data(bytearray([0xA1, 0x00, 0xA1]))
+    time.sleep(5)
+    SystemMessageCallback_usb_hs(serial, print_msg)

sciopy/sciospec_hs.py

@@ -2,7 +2,7 @@
 
 setuptools.setup(
     name="sciopy",
-    version="0.7.1",
+    version="0.7.1.3",
     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.",