UGA_Optogenetics/sequenceAcquisition.py at master · ricarvid1/UGA_Optogenetics · GitHub

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# This python code uses MicroManager device drivers to control a camera.
# Tested on Hamamatsu Orca Flash 4 camera, it acquires a sequence of images and
# stores them in a folder. ROI will also be tested.
# Code implementation: David Sanchez

#code used to get an image sequence acquisition

#Importing necessary libraries
import sys
import MMCorePy #load MicroManager for device control
import matplotlib.pyplot as plt
import time
from PIL import Image

def waitAcquisition(mmc):
    while True:
        if mmc.isSequenceRunning():
            time.sleep(0.0001)
        else:
            break

def imgNormalization(arr):
    arr = arr.astype('float')
    minVal = arr.min()
    maxVal = arr.max()
    maxLim = 2**16
    if minVal != maxVal:
        arr -= minVal
        arr *= (maxLim/(maxVal - minVal))
    return arr.astype('uint16')


if __name__ == "__main__":

    sys.path.append("C:\\Program Files\\Micro-Manager-1.4")
    #ion()

    #loading camera
    mmc = MMCorePy.CMMCore()
    #mmc.loadDevice('Camera', 'DemoCamera', 'DCam')
    #Hamamatsu
    mmc.loadDevice('Camera', 'HamamatsuHam', 'HamamatsuHam_DCAM')

    mmc.initializeAllDevices()
    mmc.setCameraDevice('Camera')


    #All figures are closed
    plt.close("all")

    #Sigle image snapshot
    #mmc.setExposure(20) #ms
    mmc.snapImage()
    img = mmc.getImage() #this is numpy array, by the way
    #plt.imshow(img, cmap='gray')
    #plt.show()

    #Region of Interest
    x = 0
    y = 0
    xSize = 512
    ySize = 512
    mmc.setROI(x,y,xSize,ySize)

    #Image sequence acquisition
    #mmc.setExposure(1)
    numImages = 5
    intervalMs = 1
    successfulAcquisition = False
    #mmc.clearCircularBuffer()
    start_time = time.time()
    mmc.prepareSequenceAcquisition('Camera')
    mmc.startSequenceAcquisition(numImages, intervalMs, True)

    #mmc.stopSequenceAcquisition('Camera')

    #waitAcquisition(mmc)
    imList = []
    # filename = "C:\\Users\\MOTIV\\Documents\\Python\\image%d.tiff" % (x,)
    filename = "sequence.tiff"
    # filename = "C:\\Users\\Administrateur\\Documents\\David\\image%d.tiff" % (x,)
    while True:
        if mmc.getRemainingImageCount() > 0:
            img = mmc.popNextImage()
            imList.append(Image.fromarray(img))
        elif not mmc.isSequenceRunning():
            if not successfulAcquisition:
                successfulAcquisition = True
                print("Acquisition finished after %s seconds" % (time.time() - start_time))
            if len(imList) == numImages:
                imList[0].save(filename, compression="None", save_all=True,
                               append_images=imList[1:])
                print("File saved after %s seconds" % (time.time() - start_time))
                break

    print("Remaining Images: %d" % mmc.getRemainingImageCount())
    #mmc.reset()
    mmc.waitForDevice('Camera')


    #SECOND ACQUISITION
    mmc.unloadDevice('Camera')
    mmc.loadDevice('Camera', 'HamamatsuHam', 'HamamatsuHam_DCAM')
    mmc.initializeAllDevices()
    mmc.setCameraDevice('Camera')

    successfulAcquisition = False
    mmc.clearCircularBuffer()
    start_time = time.time()

    mmc.prepareSequenceAcquisition('Camera')
    mmc.startSequenceAcquisition(numImages, intervalMs, True)


    imList = []
    # filename = "C:\\Users\\MOTIV\\Documents\\Python\\image%d.tiff" % (x,)
    filename = "sequence2.tiff"
    # filename = "C:\\Users\\Administrateur\\Documents\\David\\image%d.tiff" % (x,)
    while True:
        if mmc.getRemainingImageCount() > 0:
            img = mmc.popNextImage()
            imList.append(Image.fromarray(img))
        elif not mmc.isSequenceRunning():
            if not successfulAcquisition:
                successfulAcquisition = True
                print("Acquisition finished after %s seconds" % (time.time() - start_time))
            if len(imList) == numImages:
                imList[0].save(filename, compression="None", save_all=True,
                               append_images=imList[1:])
                print("File saved after %s seconds" % (time.time() - start_time))
                break

    print("Remaining Images: %d" % mmc.getRemainingImageCount())