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Imaging.py
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Imaging.py
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try:
from PIL import Image, ImageDraw # PIL & Pillow work interchangeably
except ModuleNotFoundError:
from Pillow import Image, ImageDraw
from Functions import CMaptoColor
import matplotlib.pyplot as plt
from IPython.core.display import display
import numpy as np
import pandas as pd
def ShowImage(medData, settings):
width = float(medData[0].width)
height = float(medData[0].height)
try:
CMAP = plt.get_cmap(settings[4])
except TypeError:
CMAP = plt.get_cmap('hot')
numLines = medData.shape[0]
numIntensities = medData[0].intensities.shape[0]
w = numIntensities
pixW = 1
h = int(w / width * height)
pixH = h / numLines
if pixH < 1:
pixH = 1;
h = pixH * numLines
w = int(h / height * width)
pixW = w / numIntensities
output = Image.new('RGBA', (w, h), "black")
draw = ImageDraw.Draw(output)
for smallData in medData:
i = 0
for intensity in smallData.intensities:
try:
color = CMaptoColor(CMAP(float(intensity) / medData[0].maxInt))
except ZeroDivisionError:
color = CMaptoColor(CMAP(0))
draw.rectangle(
((i * pixW, (smallData.lineNum - 1) * pixH), (i * pixW + pixW, (smallData.lineNum - 1) * pixH + pixH)),
fill=color)
i += 1
print('MZ_%0.4f DT_%0.2f' % (float(medData[0].mz), float(medData[0].driftTime)), end='')
display(output)
return()
def SaveImage(medData, settings, modifier='', AICMod=0):
width = float(medData[0].width)
height = float(medData[0].height)
try:
IMAGEFORMAT = settings[3]
CMAP = plt.get_cmap(settings[4])
except TypeError:
IMAGEFORMAT = '.png'
CMAP = plt.get_cmap('hot')
numLines = medData.shape[0]
numIntensities = medData[0].intensities.shape[0]
w = numIntensities
pixW = 1
h = int(w / width * height)
pixH = h / numLines
if pixH < 1:
pixH = 1
h = pixH * numLines
w = int(h / height * width)
pixW = w / numIntensities
output = Image.new('RGBA', (w, h), "black")
draw = ImageDraw.Draw(output)
for smallData in medData:
i = 0
for intensity in smallData.intensities:
try:
color = CMaptoColor(CMAP(float(intensity) / medData[0].maxInt))
except ZeroDivisionError:
color = CMaptoColor(CMAP(0))
draw.rectangle(
((i * pixW, (smallData.lineNum - 1) * pixH), (i * pixW + pixW, (smallData.lineNum - 1) * pixH + pixH)),
fill=color)
i += 1
if medData[0].driftTime:
outputName = ('MZ_%0.4f DT_%0.2f' % (float(medData[0].mz), float(medData[0].driftTime)))
else:
outputName = ('MZ_%0.4f' % float(medData[0].mz))
if modifier == 'Attenuate':
outputName += '_Attenuate'
elif modifier == 'Local':
outputName += '_Local'
elif modifier == 'Global':
outputName += '_Global'
elif modifier == 'AIC':
outputName += '_AIC'
if AICMod != 0:
outputName += (' ' + str(AICMod))
output.save((outputName + IMAGEFORMAT))
return()
def CreateTxtFile(medData):
if medData[0].driftTime:
outputName = ('MZ_%0.4f DT_%0.2f.txt' % (float(medData[0].mz), float(medData[0].driftTime)))
else:
outputName = ('MZ_%0.4f.txt' % float(medData[0].mz))
with open(outputName, 'w+') as file:
file.write('%i\t%i\t%s\n' % (medData[0].width, medData[0].height, medData[0].name[0:-2]))
for smallData in medData:
for intensity in smallData.intensities:
file.write(str(intensity) + ' ')
file.write('\n')
return()
def CreateRGB(bigData, save): # How to make sure that people only use 3 images from same exp
width = bigData[0][0].width # I think the file selector should limit you to images from one folder
height = bigData[0][0].height
numLines = bigData[0].shape[0]
numIntensities = bigData[0][0].intensities.shape[0]
scale1 = 255 / bigData[0][0].maxInt
scale2 = 255 / bigData[1][0].maxInt
scale3 = 255 / bigData[2][0].maxInt
w = numIntensities
pixW = 1
h = int(w / width * height)
pixH = h / numLines
if pixH < 1:
pixH = 1
h = pixH * numLines
w = int(h / height * width)
pixW = w / numIntensities
output = Image.new('RGB', (w, h), "black")
draw = ImageDraw.Draw(output)
j = 0
for smallData in bigData[2]:
i = 0
for intensity in smallData.intensities:
color = (int(intensity * scale3), int(bigData[0][j].intensities[i] * scale1),
int(bigData[1][j].intensities[i] * scale2))
draw.rectangle(
((i * pixW, (smallData.lineNum - 1) * pixH), (i * pixW + pixW, (smallData.lineNum - 1) * pixH + pixH)),
fill=color)
i += 1
j += 1
if save:
output.save(
'MZ_%0.4f DT_%0.2f %s.png' % (float(bigData[0][0].mz), float(bigData[0][0].driftTime), bigData[0][1].name))
else:
print('MZ_%0.4f DT_%0.2f' % (float(bigData[0][0].mz), float(bigData[0][0].driftTime)), end='')
display(output)
return(output)
def CreateAIC(bigData, settings, save):
width = float(bigData[0][0].width)
height = float(bigData[0][0].height)
try:
IMAGEFORMAT = settings[3]
CMAP = plt.get_cmap(settings[4])
except TypeError:
IMAGEFORMAT = '.png'
CMAP = plt.get_cmap('hot')
i = 0
for medData in bigData:
width = medData[0].width
height = medData[0].height
numLines = medData.shape[0]
numIntensities = medData[0].intensities.shape[0]
w = numIntensities
pixW = 1
h = int(w / width * height)
pixH = h / numLines
if pixH < 1:
pixH = 1;
h = pixH * numLines
w = int(h / height * width)
pixW = w / numIntensities
output = Image.new('RGBA', (w, h), "black")
draw = ImageDraw.Draw(output)
for smallData in medData:
j = 0
for intensity in smallData.intensities:
try:
color = CMaptoColor(CMAP(float(intensity) / (medData[0].maxInt)))
except ZeroDivisionError:
color = CMaptoColor(CMAP(0))
draw.rectangle(((j * pixW, (smallData.lineNum - 1) * pixH),
(j * pixW + pixW, (smallData.lineNum - 1) * pixH + pixH)), fill=color)
j += 1
if save:
output.save(('MZ_%0.4f DT_%0.2f %s' + IMAGEFORMAT) % (
float(medData[0].mz), float(medData[0].driftTime), medData[1].name))
else:
print('MZ_%0.4f DT_%0.2f' % (float(medData[0].mz), float(medData[0].driftTime)), end='')
display(output)
i += 1
return()