black formatter

1 files changed, 150 insertions, 95 deletions

diff --git a/examples/eit_with_vcsel.py b/examples/eit_with_vcsel.py
index ed0854e..3ce9d1c 100644
--- a/examples/eit_with_vcsel.py
+++ b/examples/eit_with_vcsel.py
@@ -1,6 +1,10 @@
 import logging
+
 # this should be done before justpy is called or log formatter does not work
-logging.basicConfig(format='%(asctime)s %(levelname)8s %(name)s: %(message)s', datefmt='%m/%d/%Y %H:%M:%S')
+logging.basicConfig(
+    format="%(asctime)s %(levelname)8s %(name)s: %(message)s",
+    datefmt="%m/%d/%Y %H:%M:%S",
+)
 
 import pyvisa
 import numpy as np
@@ -17,18 +21,20 @@ from qolab.hardware.daq import LabJackUE9
 from qolab.hardware.power_supply.keysight_e3612a import KeysightE3612A
 import qolab.tsdb as tsdb
 
-l = logging.getLogger('qolab.tsdb')
+l = logging.getLogger("qolab.tsdb")
 l.setLevel(logging.INFO)
-logger = logging.getLogger('Magnetometer')
+logger = logging.getLogger("Magnetometer")
 logger.setLevel(logging.INFO)
 
+
 def getConfig(apparatus):
     config = apparatus.config.copy()
     ai = apparatus.instruments
     for n, i in ai.items():
-        config[n]=i.getConfig()
+        config[n] = i.getConfig()
     return config
 
+
 class Apparatus(BasicInstrument):
     def __init__(self, *args, **kwds):
         super().__init__(*args, **kwds)
@@ -37,16 +43,20 @@ class Apparatus(BasicInstrument):
         config = self.config.copy()
         ai = self.instruments
         for n, i in ai.items():
-            config[n]=i.getConfig()
+            config[n] = i.getConfig()
         return config
 
+
 class BfieldDriver(KeysightE3612A):
-    """ need to set power supply """
+    """need to set power supply"""
+
     def __init__(self, *args, **kwds):
         super().__init__(*args, **kwds)
-        self.config['Device type'] = 'B field coil driver based on Keysight E3612A power supply'
-        self.config['Device model'] = 'v0.1'
-        self.deviceProperties.update({'B', 'Bslope_TperA', 'CoilAssignment'})
+        self.config[
+            "Device type"
+        ] = "B field coil driver based on Keysight E3612A power supply"
+        self.config["Device model"] = "v0.1"
+        self.deviceProperties.update({"B", "Bslope_TperA", "CoilAssignment"})
         """"
         Rough magnetic field calibration of the 3 axes coils in large magnetic shield
         - Ch1: 70mA -> 650 kHz shift for delta m = 2
@@ -57,12 +67,12 @@ class BfieldDriver(KeysightE3612A):
         """
         # B response to current in a given channel
         self._Bslope_TperA = {
-                1: 0.0006574710928926532,
-                2: 0.0007064314754023079,
-                3: 0.0006635058865577695
-                }
+            1: 0.0006574710928926532,
+            2: 0.0007064314754023079,
+            3: 0.0006635058865577695,
+        }
         # assuming that Ch1 controls Bz, Ch2 -> By, Ch3 -> Bx
-        self._coil_assignment = { 'chX': 3, 'chY': 2, 'chZ': 1 }
+        self._coil_assignment = {"chX": 3, "chY": 2, "chZ": 1}
 
     def getBslope_TperA(self):
         return self._Bslope_TperA
@@ -73,9 +83,9 @@ class BfieldDriver(KeysightE3612A):
     def getB(self):
         Bslope_TperA = self.getBslope_TperA()
         coil_assignment = self.getCoilAssignment()
-        chX = coil_assignment['chX']
-        chY = coil_assignment['chY']
-        chZ = coil_assignment['chZ']
+        chX = coil_assignment["chX"]
+        chY = coil_assignment["chY"]
+        chZ = coil_assignment["chZ"]
 
         Ix = self.getChanIout(chX)
         Iy = self.getChanIout(chY)
@@ -83,40 +93,43 @@ class BfieldDriver(KeysightE3612A):
         Bx = Ix * Bslope_TperA[chX]
         By = Iy * Bslope_TperA[chY]
         Bz = Iz * Bslope_TperA[chZ]
-        Bmag = float(np.sqrt(Bx*Bx + By*By + Bz*Bz))
-        theta = float(np.arccos(Bz/Bmag))
-        phi  =  float(np.arctan2(By, Bx))
-        theta_degree = float(theta/np.pi*180)
-        phi_degree = float(phi/np.pi*180)
-        return { 'Bmag': Bmag,
-                'theta': theta, 'phi': phi,
-                'theta_degree': theta_degree, 'phi_degree': phi_degree,
-                'Bx': float(Bx),
-                'By': float(By),
-                'Bz': float(Bz),
-                }
+        Bmag = float(np.sqrt(Bx * Bx + By * By + Bz * Bz))
+        theta = float(np.arccos(Bz / Bmag))
+        phi = float(np.arctan2(By, Bx))
+        theta_degree = float(theta / np.pi * 180)
+        phi_degree = float(phi / np.pi * 180)
+        return {
+            "Bmag": Bmag,
+            "theta": theta,
+            "phi": phi,
+            "theta_degree": theta_degree,
+            "phi_degree": phi_degree,
+            "Bx": float(Bx),
+            "By": float(By),
+            "Bz": float(Bz),
+        }
 
     def setB(self, Bmag=50e-6, theta=0, phi=0):
-        """ Sets B field currents based on B (in T) and angles theta, and phi """
+        """Sets B field currents based on B (in T) and angles theta, and phi"""
         self._Bmag = Bmag
         self._theta = theta
         self._phi = phi
 
-        Bx = Bmag*np.sin(theta)*np.cos(phi)
-        By = Bmag*np.sin(theta)*np.sin(phi)
-        Bz = Bmag*np.cos(theta)
+        Bx = Bmag * np.sin(theta) * np.cos(phi)
+        By = Bmag * np.sin(theta) * np.sin(phi)
+        Bz = Bmag * np.cos(theta)
 
         Bslope_TperA = self.getBslope_TperA()
         coil_assignment = self.getCoilAssignment()
-        chX = coil_assignment['chX']
-        chY = coil_assignment['chY']
-        chZ = coil_assignment['chZ']
+        chX = coil_assignment["chX"]
+        chY = coil_assignment["chY"]
+        chZ = coil_assignment["chZ"]
 
         Ix = Bx / Bslope_TperA[chX]
         Iy = By / Bslope_TperA[chY]
         Iz = Bz / Bslope_TperA[chZ]
 
-        logger.info(f'Setting {Bmag=}, {theta=} {phi=} in radians')
+        logger.info(f"Setting {Bmag=}, {theta=} {phi=} in radians")
         logger.info(f"Setting {chX=} to {Ix}")
         logger.info(f"Setting {chY=} to {Iy}")
         logger.info(f"Setting {chZ=} to {Iz}")
@@ -126,69 +139,92 @@ class BfieldDriver(KeysightE3612A):
         return Ix, Iy, Iz
 
     def setBinDegrees(self, Bmag=50e-6, theta=0, phi=0):
-        logger.info(f'Setting {Bmag=},  {theta=} {phi=} in degrees')
-        return self.setB(Bmag=Bmag, theta=theta/180*np.pi, phi=phi/180*np.pi)
+        logger.info(f"Setting {Bmag=},  {theta=} {phi=} in degrees")
+        return self.setB(Bmag=Bmag, theta=theta / 180 * np.pi, phi=phi / 180 * np.pi)
+
 
 # TSDB logger setting
-tsdb_client = tsdb.Client('influx', 'http://lumus.physics.wm.edu:8428', database='qolab')
-tsdb_ingester = tsdb.Ingester(tsdb_client, batch=11, measurement_prefix='VAMPIRE.VCSEL')
+tsdb_client = tsdb.Client(
+    "influx", "http://lumus.physics.wm.edu:8428", database="qolab"
+)
+tsdb_ingester = tsdb.Ingester(tsdb_client, batch=11, measurement_prefix="VAMPIRE.VCSEL")
 
 # creating Apparatus with all instruments to be logged
-app_nickname = 'magnetometer'
-apparatus = Apparatus(tsdb_ingester=tsdb_ingester, device_nickname=app_nickname,)
-apparatus.config['Device type'] = 'QOL VAMPIRE VCSEL magnetometer'
-apparatus.config['Device model'] = 'v0.1'
-apparatus.config['FnamePrefix'] = 'magnetometer_eit'
+app_nickname = "magnetometer"
+apparatus = Apparatus(
+    tsdb_ingester=tsdb_ingester,
+    device_nickname=app_nickname,
+)
+apparatus.config["Device type"] = "QOL VAMPIRE VCSEL magnetometer"
+apparatus.config["Device model"] = "v0.1"
+apparatus.config["FnamePrefix"] = "magnetometer_eit"
 # apparatus.config['SavePath'] = '/mnt/qol_grp_data/data.VAMPIRE.VCSEL'
-apparatus.config['SavePath'] = './data'
+apparatus.config["SavePath"] = "./data"
 
 
 logger.info("Accessing hardware")
 rm = pyvisa.ResourceManager()
-instr=rm.open_resource('USB0::10893::4354::MY61001869::0::INSTR')
-Bfield = BfieldDriver(instr, device_nickname='.'.join([app_nickname, 'b_field_driver']), tsdb_ingester=tsdb_ingester)
+instr = rm.open_resource("USB0::10893::4354::MY61001869::0::INSTR")
+Bfield = BfieldDriver(
+    instr,
+    device_nickname=".".join([app_nickname, "b_field_driver"]),
+    tsdb_ingester=tsdb_ingester,
+)
 # ps = KeysightE3612A(instr, device_nickname='.'.join([app_nickname, 'coil_driver']), tsdb_ingester=tsdb_ingester)
-ps = Bfield # alias
+ps = Bfield  # alias
 # set safety current limit
-ps.setChanIlimit(1, 0.1) # max current in Amps
-ps.setChanIlimit(2, 0.1) # max current in Amps
-ps.setChanIlimit(3, 0.1) # max current in Amps
+ps.setChanIlimit(1, 0.1)  # max current in Amps
+ps.setChanIlimit(2, 0.1)  # max current in Amps
+ps.setChanIlimit(3, 0.1)  # max current in Amps
 
-if platform.system() == 'Linux':
-    rfgen_port='/dev/ttyUSB0'
+if platform.system() == "Linux":
+    rfgen_port = "/dev/ttyUSB0"
 else:
-    rfgen_port='COM4'
-rfgen = QOL_LMX2487(port=rfgen_port, speed=115200, timeout=1, device_nickname='.'.join([app_nickname, 'rfgen']), tsdb_ingester=tsdb_ingester)
+    rfgen_port = "COM4"
+rfgen = QOL_LMX2487(
+    port=rfgen_port,
+    speed=115200,
+    timeout=1,
+    device_nickname=".".join([app_nickname, "rfgen"]),
+    tsdb_ingester=tsdb_ingester,
+)
 
 
-daq = LabJackUE9(device_nickname='.'.join([app_nickname, 'daq']), tsdb_ingester=tsdb_ingester)
+daq = LabJackUE9(
+    device_nickname=".".join([app_nickname, "daq"]), tsdb_ingester=tsdb_ingester
+)
 
 logger.info("Adding instruments to apparatus")
-apparatus.instruments={}
+apparatus.instruments = {}
 ai = apparatus.instruments
-ai['rfgen'] = rfgen
-ai['daq']   = daq
-ai['b_field_driver'] = Bfield
+ai["rfgen"] = rfgen
+ai["daq"] = daq
+ai["b_field_driver"] = Bfield
 
 
-logger.info('Setting magnetic field coils currents')
+logger.info("Setting magnetic field coils currents")
 # ps.setChanIout_mA(1, 70)
 # ps.setChanIout_mA(2, 0)
 # ps.setChanIout_mA(3, 0)
-logger.info('Done setting magnetic field coils currents')
+logger.info("Done setting magnetic field coils currents")
 
-def eitSweep(central_frequency, frequency_span, Np, Nsweeps=1):
-    frList = np.linspace(central_frequency-frequency_span/2, central_frequency+frequency_span/2, Np)
-    trFreq=Trace('Frequency')
-    trFreq.config['unit']='Hz'
-    trTransmission=Trace('Transmission')
-    trTransmission.config['unit']='Arb. Unit'
-    trLockin=Trace('Lockin')
-    trLockin.config['unit']='V'
-
-    trEIT = TraceSetSameX('EIT')
 
-    for sw in pbar(range(1,Nsweeps+1), desc="Sweep"):
+def eitSweep(central_frequency, frequency_span, Np, Nsweeps=1):
+    frList = np.linspace(
+        central_frequency - frequency_span / 2,
+        central_frequency + frequency_span / 2,
+        Np,
+    )
+    trFreq = Trace("Frequency")
+    trFreq.config["unit"] = "Hz"
+    trTransmission = Trace("Transmission")
+    trTransmission.config["unit"] = "Arb. Unit"
+    trLockin = Trace("Lockin")
+    trLockin.config["unit"] = "V"
+
+    trEIT = TraceSetSameX("EIT")
+
+    for sw in pbar(range(1, Nsweeps + 1), desc="Sweep"):
         for fr in pbar(frList, desc="Freq Scan"):
             rfgen.setFreqFixed(float(fr))
             time.sleep(dwellTime)
@@ -204,66 +240,85 @@ def eitSweep(central_frequency, frequency_span, Np, Nsweeps=1):
     trEIT.addTrace(trTransmission)
     trEIT.addTrace(trLockin)
 
-    trEIT.config['tags']['apparatus']=apparatus.getConfig()
+    trEIT.config["tags"]["apparatus"] = apparatus.getConfig()
 
     return trEIT
 
+
 def getCurrentCalibrationData(ch=1):
     curList = [20, 30, 40, 50, 60, 70, 80, 90, 100, 110]
     ps.setChanIout_mA(1, 0)
     ps.setChanIout_mA(2, 0)
     ps.setChanIout_mA(3, 0)
     for current in curList:
-        logger.info(f'Preparing data for {current=} in {ch=} ready')
+        logger.info(f"Preparing data for {current=} in {ch=} ready")
         ps.setChanIout_mA(ch, current)
         trEIT = eitSweep(central_frequency, frequency_span, Np, Nsweeps=Nsweeps)
         trEIT.plot()
         fn = apparatus.getNextDataFile()
-        logger.info(f'Data ready for {current=} in {ch=}')
-        logger.info(f'Data saved to {fn=}')
+        logger.info(f"Data ready for {current=} in {ch=}")
+        logger.info(f"Data saved to {fn=}")
         trEIT.save(fn)
 
+
 def calibrateCoilsCurrent():
-    Np=1000
-    Nsweeps=5
+    Np = 1000
+    Nsweeps = 5
     getCurrentCalibrationData(ch=1)
     getCurrentCalibrationData(ch=2)
     getCurrentCalibrationData(ch=3)
 
-def setBandTakeTrace(Bmag=50e-6, theta=0, phi=0, central_frequency=6.83468e9, frequency_span=2500e3, Np=100, Nsweeps=1):
-    """ theta and phi assumed to be in degrees """
+
+def setBandTakeTrace(
+    Bmag=50e-6,
+    theta=0,
+    phi=0,
+    central_frequency=6.83468e9,
+    frequency_span=2500e3,
+    Np=100,
+    Nsweeps=1,
+):
+    """theta and phi assumed to be in degrees"""
     Bfield.setBinDegrees(Bmag=Bmag, theta=theta, phi=phi)
     trEIT = eitSweep(central_frequency, frequency_span, Np, Nsweeps=Nsweeps)
     return trEIT
 
 
 def rotateBandGetEITtrace():
-    Np=500
-    Nsweeps=5
-    Bmag=50e-6 # earth magnetic field in Tesla (0.5 G)
+    Np = 500
+    Nsweeps = 5
+    Bmag = 50e-6  # earth magnetic field in Tesla (0.5 G)
     phiStep = 10
     thetaStep = 10
-    phiSet = range(0,90+phiStep, phiStep)
-    thetaSet = range(0,90+thetaStep, thetaStep)
+    phiSet = range(0, 90 + phiStep, phiStep)
+    thetaSet = range(0, 90 + thetaStep, thetaStep)
     for phi in phiSet:
         for theta in thetaSet:
-            trEIT = setBandTakeTrace(Bmag=Bmag, theta=theta, phi=phi, central_frequency=central_frequency, frequency_span=frequency_span, Np=Np, Nsweeps=Nsweeps)
+            trEIT = setBandTakeTrace(
+                Bmag=Bmag,
+                theta=theta,
+                phi=phi,
+                central_frequency=central_frequency,
+                frequency_span=frequency_span,
+                Np=Np,
+                Nsweeps=Nsweeps,
+            )
             plt.clf()
             trEIT.plot()
             plt.draw()
             plt.pause(0.1)
             fn = apparatus.getNextDataFile()
-            logger.info(f'Data ready for {Bmag=} in {theta=} {phi=}')
-            logger.info(f'Data saved to {fn=}')
+            logger.info(f"Data ready for {Bmag=} in {theta=} {phi=}")
+            logger.info(f"Data saved to {fn=}")
             trEIT.save(fn)
 
 
 central_frequency = 6.83468e9
-frequency_span =  2500e3
+frequency_span = 2500e3
 
-dwellTime=0.1
-Np=100
-Nsweeps=1
+dwellTime = 0.1
+Np = 100
+Nsweeps = 1
 
 
 tsdb_ingester.commit()