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ZGainsforth/AcquireStack.py

Created May 11, 2023 23:08
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  1. ZGainsforth created this gist May 11, 2023.
    151 changes: 151 additions & 0 deletions AcquireStack.py
    View file
    Original file line number Diff line number Diff line change
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    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()