Js get cv

.gitignore

@@ -37,4 +37,5 @@
 .Spotlight-V100
 .Trashes
 ehthumbs.db
-Thumbs.db
+Thumbs.db
+Icon

FrgTools/frgtools/.ipynb_checkpoints/cyclicvolt-checkpoint.py

@@ -0,0 +1,163 @@
+# getCV
+"""
+Loads CV data from a text file. Pulls the last curve out of the
+repeats (red/ox cycle).
+
+Example: mydata = getCV(use UI to select file)
+
+		 mydata = getCV ('C:\Myname\CV\File.ras')   (directly offer fpath)
+
+Output: Structure with J and V from the final run, along with all other associated data in text file.
+    mydata['v'] --> voltage
+    mydata['j'] --> current density
+        ['header'] --> all info from the header
+        ['area']
+        ['date']
+        ['time']
+        ['num_cycles']
+        ['cathodic_peak'] --> onset potential method 1
+        ['anodic_peak'] --> anodic peak current (at the right most end (highest positive potential))
+        ['inflection_onset'] --> onset method 2
+        ['intersect_onset'] --> onset method 3
+        ['scans'] --> 
+            [j][#]
+            [v][#]
+
+
+Onset potential methods: 
+	1: Direct minimum
+	2: Inflection point
+	3: Intersection at baseline
+
+"""
+import os
+import numpy as np
+import csv
+# from .plotting import directionalplot
+
+def getCV(fpath, area =1):
+    cvdata = load_cv(fpath)
+    cvdata = getOnsetPotentials(cvdata)
+    return cvdata
+
+def load_cv(fpath, area = 1):
+	# headerkey = {
+	#     'Run on channel': 'channel',
+	#     'Electrode connection': 'electrode_connection',
+	#     'Ewe,I filtering': 'ewe_ifilter',
+	#     'Channel': 'channel',
+	#     'Acquisition started on': 'datetime',
+	#     'Reference electrode': 'ref_electrode',
+	# }
+
+
+	DATA_START = 'mode\tox/red\terror'
+
+	data = {
+		'v': None,
+		'j': None,
+		'numscans': None,
+		'area': area,
+		'scans': {},
+		'header': {}
+	}
+
+	key = None
+	previouskey = None
+	with open(fpath, 'r', errors = 'ignore', encoding = 'utf-8') as f:
+		headerlines = 54 #initial guess, will get picked up in code at 
+		line = f.readline()#.decode('utf-8')
+		while not line.startswith(DATA_START):
+			if line.startswith('Acquisition started on'):
+				data['date'], data['time'] = line.split(' : ')[1].split(' ')
+			else:
+				if ' : ' in line:
+					key, value = line.split(' : ')
+					data['header'][key.strip()] = value.strip()
+				elif '  ' in line:
+					parts = line.strip().split('  ')
+					key = parts[0]
+					value = parts[-1]
+					if key == 'vs.':
+						data['header'][previouskey] += ' vs. {}'.format(value.strip())
+					else:
+						data['header'][key.strip()] = value.strip()
+				previouskey = key
+			line = f.readline()#.decode('utf-8')
+
+		colnames = []
+		for c in line.strip().split('\t'):
+			if c == 'ox/red':
+				colnames.append(c)
+			elif c.startswith('<I>'):
+				colnames.append('i')
+			elif c.startswith('Ewe'):
+				colnames.append('v')
+			elif c.startswith('cycle'):
+				colnames.append('cycle')
+			else:
+				colnames.append(c.split('/')[0])
+		f_reader = csv.DictReader(f, fieldnames = colnames, delimiter = '\t')  
+		data['scans'] = {k:[[]] for k in colnames}
+		currentcycle = 1
+		for row in f_reader:
+			if int(row['cycle']) > currentcycle:
+				currentcycle = int(row['cycle'])
+				for k in data['scans'].keys():
+					data['scans'][k].append([])
+			for k, val in row.items():
+				data['scans'][k][currentcycle-1].append(float(val))
+
+		data['scans'] = {k:[np.array(cycledata) for cycledata in v] for k,v in data['scans'].items()}
+		data['scans']['j'] = [i/area for i in data['scans']['i']]
+		data['num_cycles'] = currentcycle
+		data['v'] = data['scans']['v'][-1]
+		data['j'] = data['scans']['j'][-1]
+
+		return data
+
+def getOnsetPotentials(cvdata,fitwidth = 40):
+    # Finding cathodic peak voltage
+    X = cvdata['v']
+    Y = cvdata['j']
+    idx0 = np.argmin(Y)
+    cvdata['cathodic_peak'] = X[idx0] 
+
+    # Finding anodic peak current at the end of the voltammogram
+    idx1 = np.argmax(X)
+    cvdata['anodic_peak'] = Y[idx1] 
+
+    # Inflection point onset
+    idx2 = np.argmin(X)
+    XX = X[idx1+500 : idx2 - 20]
+    YY = Y[idx1+500 : idx2 - 20]
+
+    dydx = np.gradient(YY)/np.gradient(XX) # Finds first derivative, delta y/ delta x
+    dydx = smooth(dydx)
+
+    idx3 = np.argmax(dydx) # Inflection point on the cathodic curve
+    idx4 = np.argmin(abs(YY)) # Getting closest to the baseline center as possible
+    cvdata['inflection_onset'] = XX[idx3]
+
+    X_ = XX[idx3 - fitwidth//2: idx3 + fitwidth//2]
+    Y_ = YY[idx3 - fitwidth//2: idx3 + fitwidth//2]
+    linfit_3 = np.polyfit(X_,Y_,1)
+
+    X_ = XX[idx4 - fitwidth//2: idx4 + fitwidth//2]
+    Y_ = YY[idx4 - fitwidth//2: idx4 + fitwidth//2]
+    linfit_4 = np.polyfit(X_,Y_,1)
+
+    intersect_x = (linfit_4[1] - linfit_3[1]) / (linfit_3[0] - linfit_4[1])
+    intersect_y = linfit_3[0] * intersect_x + linfit_3[1]
+    cvdata['intersect_onset'] = [intersect_x, intersect_y]
+    return cvdata
+
+def smooth(a,WSZ=5):
+    # a: NumPy 1-D array containing the data to be smoothed
+    # WSZ: smoothing window size needs, which must be odd number,
+    # as in the original MATLAB implementation
+    out0 = np.convolve(a,np.ones(WSZ,dtype=int),'valid')/WSZ    
+    r = np.arange(1,WSZ-1,2)
+    start = np.cumsum(a[:WSZ-1])[::2]/r
+    stop = (np.cumsum(a[:-WSZ:-1])[::2]/r)[::-1]
+    return np.concatenate((  start , out0, stop  ))

FrgTools/frgtools/cyclicvolt.py

@@ -0,0 +1,163 @@
+# getCV
+"""
+Loads CV data from a text file. Pulls the last curve out of the
+repeats (red/ox cycle).
+
+Example: mydata = getCV(use UI to select file)
+
+		 mydata = getCV ('C:\Myname\CV\File.ras')   (directly offer fpath)
+
+Output: Structure with J and V from the final run, along with all other associated data in text file.
+    mydata['v'] --> voltage
+    mydata['j'] --> current density
+        ['header'] --> all info from the header
+        ['area']
+        ['date']
+        ['time']
+        ['num_cycles']
+        ['cathodic_peak'] --> onset potential method 1
+        ['anodic_peak'] --> anodic peak current (at the right most end (highest positive potential))
+        ['inflection_onset'] --> onset method 2
+        ['intersect_onset'] --> onset method 3
+        ['scans'] --> 
+            [j][#]
+            [v][#]
+
+
+Onset potential methods: 
+	1: Direct minimum
+	2: Inflection point
+	3: Intersection at baseline
+
+"""
+import os
+import numpy as np
+import csv
+# from .plotting import directionalplot
+
+def getCV(fpath, area =1):
+    cvdata = load_cv(fpath)
+    cvdata = getOnsetPotentials(cvdata)
+    return cvdata
+
+def load_cv(fpath, area = 1):
+	# headerkey = {
+	#     'Run on channel': 'channel',
+	#     'Electrode connection': 'electrode_connection',
+	#     'Ewe,I filtering': 'ewe_ifilter',
+	#     'Channel': 'channel',
+	#     'Acquisition started on': 'datetime',
+	#     'Reference electrode': 'ref_electrode',
+	# }
+
+
+	DATA_START = 'mode\tox/red\terror'
+
+	data = {
+		'v': None,
+		'j': None,
+		'numscans': None,
+		'area': area,
+		'scans': {},
+		'header': {}
+	}
+
+	key = None
+	previouskey = None
+	with open(fpath, 'r', errors = 'ignore', encoding = 'utf-8') as f:
+		headerlines = 54 #initial guess, will get picked up in code at 
+		line = f.readline()#.decode('utf-8')
+		while not line.startswith(DATA_START):
+			if line.startswith('Acquisition started on'):
+				data['date'], data['time'] = line.split(' : ')[1].split(' ')
+			else:
+				if ' : ' in line:
+					key, value = line.split(' : ')
+					data['header'][key.strip()] = value.strip()
+				elif '  ' in line:
+					parts = line.strip().split('  ')
+					key = parts[0]
+					value = parts[-1]
+					if key == 'vs.':
+						data['header'][previouskey] += ' vs. {}'.format(value.strip())
+					else:
+						data['header'][key.strip()] = value.strip()
+				previouskey = key
+			line = f.readline()#.decode('utf-8')
+
+		colnames = []
+		for c in line.strip().split('\t'):
+			if c == 'ox/red':
+				colnames.append(c)
+			elif c.startswith('<I>'):
+				colnames.append('i')
+			elif c.startswith('Ewe'):
+				colnames.append('v')
+			elif c.startswith('cycle'):
+				colnames.append('cycle')
+			else:
+				colnames.append(c.split('/')[0])
+		f_reader = csv.DictReader(f, fieldnames = colnames, delimiter = '\t')  
+		data['scans'] = {k:[[]] for k in colnames}
+		currentcycle = 1
+		for row in f_reader:
+			if int(row['cycle']) > currentcycle:
+				currentcycle = int(row['cycle'])
+				for k in data['scans'].keys():
+					data['scans'][k].append([])
+			for k, val in row.items():
+				data['scans'][k][currentcycle-1].append(float(val))
+
+		data['scans'] = {k:[np.array(cycledata) for cycledata in v] for k,v in data['scans'].items()}
+		data['scans']['j'] = [i/area for i in data['scans']['i']]
+		data['num_cycles'] = currentcycle
+		data['v'] = data['scans']['v'][-1]
+		data['j'] = data['scans']['j'][-1]
+
+		return data
+
+def getOnsetPotentials(cvdata,fitwidth = 40):
+    # Finding cathodic peak voltage
+    X = cvdata['v']
+    Y = cvdata['j']
+    idx0 = np.argmin(Y)
+    cvdata['cathodic_peak'] = X[idx0] 
+
+    # Finding anodic peak current at the end of the voltammogram
+    idx1 = np.argmax(X)
+    cvdata['anodic_peak'] = Y[idx1] 
+
+    # Inflection point onset
+    idx2 = np.argmin(X)
+    XX = X[idx1+500 : idx2 - 20]
+    YY = Y[idx1+500 : idx2 - 20]
+
+    dydx = np.gradient(YY)/np.gradient(XX) # Finds first derivative, delta y/ delta x
+    dydx = smooth(dydx)
+
+    idx3 = np.argmax(dydx) # Inflection point on the cathodic curve
+    idx4 = np.argmin(abs(YY)) # Getting closest to the baseline center as possible
+    cvdata['inflection_onset'] = XX[idx3]
+
+    X_ = XX[idx3 - fitwidth//2: idx3 + fitwidth//2]
+    Y_ = YY[idx3 - fitwidth//2: idx3 + fitwidth//2]
+    linfit_3 = np.polyfit(X_,Y_,1)
+
+    X_ = XX[idx4 - fitwidth//2: idx4 + fitwidth//2]
+    Y_ = YY[idx4 - fitwidth//2: idx4 + fitwidth//2]
+    linfit_4 = np.polyfit(X_,Y_,1)
+
+    intersect_x = (linfit_4[1] - linfit_3[1]) / (linfit_3[0] - linfit_4[1])
+    intersect_y = linfit_3[0] * intersect_x + linfit_3[1]
+    cvdata['intersect_onset'] = [intersect_x, intersect_y]
+    return cvdata
+
+def smooth(a,WSZ=5):
+    # a: NumPy 1-D array containing the data to be smoothed
+    # WSZ: smoothing window size needs, which must be odd number,
+    # as in the original MATLAB implementation
+    out0 = np.convolve(a,np.ones(WSZ,dtype=int),'valid')/WSZ    
+    r = np.arange(1,WSZ-1,2)
+    start = np.cumsum(a[:WSZ-1])[::2]/r
+    stop = (np.cumsum(a[:-WSZ:-1])[::2]/r)[::-1]
+    return np.concatenate((  start , out0, stop  ))

FrgTools/frgtools/misc.py

@@ -1,5 +1,6 @@
 import os
 from tqdm import tqdm
+import re
 
 def listdir(path = '.', display = True):
 	exclude = ['desktop.ini']
@@ -39,6 +40,44 @@ def searchdir(path = '.', find = [], ignore = ['desktop.ini'], fids = [], match_
 	fids = []
 	return temp
 
+def natsort(l):
+    """
+    Input a list (os.listdir(path))
+    Natsort will sort list 'l' as windows does. 
+
+    Example:
+    List: [PL1, PL10, PL11, PL2, PL3]
+	natsort(List) -> [PL1,PL2,PL3,PL10,PL11]
+    """
+    convert = lambda text: int(text) if text.isdigit() else text
+    alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ]
+    l.sort( key=alphanum_key )
+    return l
+
+
+# load video numpy array
+import cv2
+import numpy as np
+
+def load_video(fpath):
+	"""
+	Loads a video, returns frame by frame as numpy array
+
+	fpath: string, filepath to video file.
+	"""
+	cap = cv2.VideoCapture(filename = fpath)
+	frames = []
+	cap.open(filename = fpath)
+	while (cap.isOpened()):
+		ret,frame = cap.read()
+		if not ret:
+			break
+		gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
+		frames.append(gray)
+	cap.release()
+	return np.array(frames)
+
+
 ### script to send email from generic FRG alert address
 import smtplib
 from email.mime.text import MIMEText