Using Tescan SharkSEM interface, acquire a stack of images rapidly in sequence.

AcquireStack.py

import pdb
import os
import sys
sys.path.append(os.path.join('..', 'remote'))
import time
import sem
import struct
import base64
from sem_v3_lib import *


print("Script Starting")

xpixels = 512 # pixels
ypixels = 512
ViewField = 20
# microns
NumFrames = 50
ScanSpeed = 6
SampleName = 'Track 220 TP2'
BitsPerPixel = 16
AcquireBSE = True
AcquireSE = False
TimeoutSeconds = 100 # Maximum number of seconds to wait in infinite loop before bailing.

if AcquireBSE == True and AcquireSE == True:
    print('For now, you must choose only BSE or SE.  Later write code to branch the output based on the channel (str[v[1] in WriteImage).')
    sys.exit()
#
# read SharkSEM message from data connection (callbacks)
#
# return:   (message name, message body)
#
def ReadMessage(conn):

    # receive the message header
    msg_name = conn._RecvStrD(16)
    hdr = conn._RecvStrD(16)
    v = struct.unpack("<IIHHI", hdr)
    body_size = v[0]
    
    # get fn name
    cb_name = DecodeString(msg_name)
                                
    # receive the body
    cb_body = conn._RecvStrD(body_size)
        
    # finished reading message
    return (cb_name, cb_body)

def WriteImage(m, file):
    #pdb.set_trace()
    bytes_read = 0
    ReadTimeStart = time.time()
    while bytes_read < xpixels*ypixels*BitsPerPixel/8:
        #print(time.time() - ReadTimeStart)
        if (time.time() - ReadTimeStart) > TimeoutSeconds:
            print('Timeout is getting image data.')
            return
        #print("Read...")
        try:
            (cb_name, cb_body) = ReadMessage(m.connection)
        except e:
            print(e)
        #time.sleep(0.002)
        #print(cb_name)
        #print(cb_body)
        
        v = struct.unpack("<IiIiI", cb_body[0:20])
        #print("Frame: " + str(v[0]))
        #print("Channel: " + str(v[1]))
        #print("Index: " + str(v[2]))
        #print("BPP: " + str(v[3]))
        #print("Writing " + str(v[4]) + " bytes")

        #pdb.set_trace()
        bytes_read = bytes_read + file.write(cb_body[20:])

        #print("Bytes read: " + str(bytes_read))

        if bytes_read >= xpixels*ypixels*BitsPerPixel/8:        
            return


def main():

    m = sem.Sem()
    conn = m.Connect('localhost', 8300)
    if conn<0:
        print("Error: Unable to connect to SEM")
        return

    # Make sure channel 0 is BSE
    m.DtSelect(0,1)
    time.sleep(0.2)
    # Make sure channel 1 is SE
    m.DtSelect(1,0)
    time.sleep(0.2)
    if AcquireSE == True:
        m.DtEnable(1, 1, BitsPerPixel)
    else:
        m.DtEnable(1, 0)
    if AcquireBSE == True:
        m.DtEnable(0, 1, BitsPerPixel)
    else:
        m.DtEnable(0, 0)
    time.sleep(0.2)
        
    print(m.DtEnumDetectors())
    print('Detector 0 [enable, bpp] = ' + str(m.DtGetEnabled(0)))
    print('Detector 1 [enable, bpp] = ' + str(m.DtGetEnabled(1)))
    #print(m.DtGetEnabled(1))
    #return

    # make sure scanning is inactive
    m.ScStopScan()
    time.sleep(0.5)

    # Scan Speed.
    print('Setting scan speed to '+str(ScanSpeed))
    m.ScSetSpeed(ScanSpeed)
    time.sleep(0.5)

    # Get the view field
    print('Setting view field to '+str(ViewField)+' microns.')
    m.SetViewField(ViewField/1000)
    time.sleep(1.0)

    FileName = SampleName+' - '+str(xpixels)+'x'+str(ypixels)+'x'+str(NumFrames)+', ViewField='+str(ViewField)+' um, BSE='+str(AcquireBSE)+', SE='+str(AcquireSE)+', BPP='+str(BitsPerPixel)+', Little Endian.raw'
    print('Saving to '+FileName)

    # Open output file and start saving
    if os.path.exists(FileName):
        os.remove(FileName)
    file = open(FileName, "wb")

    try:
        for i in range(NumFrames):
            print("Scanning "+str(i+1)+" of "+str(NumFrames)+".")
            # Scan the image
            m.ScScanXY(1, xpixels, ypixels, 0, 0, xpixels-1, ypixels-1, 1)
            time.sleep(0.2)
            # And save it.
            WriteImage(m, file)
            time.sleep(0.2)
    finally:
        file.close()
    
    print("Done")

main()