Test Micropoint calibration with configurable pattern for e.g. 365nm objective

generate_test_ROI_for_micropoint.py

'''
Generate an Andor iQ .rgn file with a scalable and repositionable pattern of 
FRAPPA points
'''

# User variables
SENSOR_SIZE = [512, 512]
CENTER = [255,255]
SIDE_LENGTH = 360
POINT_SPACING = 20
##FILE_PATH = r'Kinetic Imaging/iQx/Default'
FILE_PATH = r'Desktop'
FILE_NAME = 'micropoint_pattern'
LOG_FILE_NAME = r'micropoint_pattern.log'
P = POINT_SPACING
LINE_POINTS = SIDE_LENGTH / POINT_SPACING
LOCAL_STAR_PATTERN = [
  [0,0],
  [-P, -P],
  [-P, P],
  [P, P],
  [P, -P]
]


from os import path
import logging


logging.basicConfig(filename=LOG_FILE_NAME, level=logging.DEBUG)


def line(start, end):
    '''
    Return [x, y] array between start and end; both inclusive
    '''
    logging.info('Making line: ' + repr(start) + ' ' + repr(end))
    
    negative_x = False
    negative_y = False
    
    if start[0] > end[0]: negative_x = True
    if start[1] > end[1]: negative_y = True
    
    if negative_x:
        spacing_x = (start[0] - end[0]) / LINE_POINTS
        if spacing_x == 0:
            x = [start[0]] * (LINE_POINTS + 1)
        else:
            x = range(start[0], end[0] -spacing_x, -spacing_x)
        logging.debug('x: ' + repr(x))
    else:
        spacing_x = (end[0] - start[0]) / LINE_POINTS
        if spacing_x == 0:
            x = [start[0]] * (LINE_POINTS + 1)
        else:
            x = range(start[0], end[0] +spacing_x, +spacing_x)
        logging.debug('x: ' + repr(x))
    
    if negative_y:
        spacing_y = (start[1] - end[1]) / LINE_POINTS
        if spacing_y == 0:
            y = [start[1]] * (LINE_POINTS + 1)
        else:
            y = range(start[1], end[1] -spacing_y, -spacing_y)
        logging.debug('y: ' + repr(y))
    else:
        spacing_y = (end[1] - start[1]) / LINE_POINTS
        if spacing_y == 0:
            y = [start[1]] * (LINE_POINTS + 1)
        else:
            y = range(start[1], end[1] +spacing_y, +spacing_y)
        logging.debug('y: ' + repr(y))
    
    return zip(x, y)


def point_generator(center = CENTER,
                      side_length = SIDE_LENGTH):
    '''
    Create cross hair pattern, and star patterns around cross hair
    '''
    points = []
    
    h = SIDE_LENGTH / 2    
    cx = CENTER[0]
    cy = CENTER[1]
    
    # Draw diagonals
    top_left = [cx-h, cy-h]
    top_right = [cx+h, cy-h]
    bottom_left = [cx-h, cy+h]
    bottom_right = [cx+h, cy+h]
    
    points += line(top_left, bottom_right)
    points += line(bottom_left, top_right)
    
    
    # Draw straights
    v1 = cx - 2*POINT_SPACING
    v2 = cx + 2*POINT_SPACING
    h1 = cy - 2*POINT_SPACING
    h2 = cy + 2*POINT_SPACING
    
    points += line([v1, cy-h], [v1, cy+h])
    points += line([v2, cy-h], [v2, cy+h])
    points += line([cx-h, h1], [cx+h, h1])
    points += line([cx-h, h2], [cx+h, h2])
    
    # prune duplicate points
    points = list(set(points))
    
    return points


def existspath(mypath):
  '''
  Return 1 if file or path exists, else return 0
  '''
  if path.exists(mypath):
    logging.info('Found path %s' % mypath)
    return 1
  else:
    logging.error('Could not find path %s' % mypath)
    return 0


def main():
    
    points = point_generator()
    n = len(points)
    
    ## FIXME: Set date and time to current
    HEADER = \
    '''[Phase List 5.0]
Number Of Phases=4
Date=12/1/2011
Time=2:18:28 PM
Phase0 Name=_Background
Phase0 Colour=255
Phase0 Grey Min=255
Phase0 Grey Max=0
Phase0 Red Min=255
Phase0 Red Max=0
Phase0 Green Min=255
Phase0 Green Max=0
Phase0 Blue Min=255
Phase0 Blue Max=0
Phase0 Enabled=1
Phase1 Name=_Crop
Phase1 Colour=16711680
Phase1 Grey Min=255
Phase1 Grey Max=0
Phase1 Red Min=255
Phase1 Red Max=0
Phase1 Green Min=255
Phase1 Green Max=0
Phase1 Blue Min=255
Phase1 Blue Max=0
Phase1 Enabled=1
Phase2 Name=_Cycle
Phase2 Colour=16777215
Phase2 Grey Min=255
Phase2 Grey Max=0
Phase2 Red Min=255
Phase2 Red Max=0
Phase2 Green Min=255
Phase2 Green Max=0
Phase2 Blue Min=255
Phase2 Blue Max=0
Phase2 Enabled=1
Phase3 Name=_FRAPPA
Phase3 Colour=65535
Phase3 Grey Min=255
Phase3 Grey Max=0
Phase3 Red Min=255
Phase3 Red Max=0
Phase3 Green Min=255
Phase3 Green Max=0
Phase3 Blue Min=255
Phase3 Blue Max=0
Phase3 Enabled=1

[Region List 4.0]
'''
    
    # Change as appropriate
    NUMBER_OF_REGIONS = 'Number Of Regions={0}\n'.format(n)
    
    ## FIME: Set date and time to current
    DATE_TIME = \
    '''Date=12/1/2011
Time=2:18:28 PM'''
    
    
    # Create zip file name
    logging.debug('Creating region file name')
    ##desktop_path = path.join(path.expandvars("%ALLUSERSAPPDATA%"), FILE_PATH)
    desktop_path = path.join(path.expanduser("~"), FILE_PATH)
    FILE = path.join(desktop_path, FILE_NAME)
    FILE = ''.join([FILE, '.rgn'])
    logging.info('Writing to region file: ' + FILE)
    
    ## FIXME:  prevent file collision!
    rfile = open(FILE, 'w')
    rfile.write(HEADER + \
                NUMBER_OF_REGIONS + \
                DATE_TIME)
    
    label = 1
    
    for point in points:
    
        REGION = '''
Region{0} Label={0}
Region{0} Class Name=_FRAPPA
Region{0} Overlay Type=1
Region{0} Overlay Colour=65535
Region{0} Overlay Line Width=0
Region{0} Number Of Points=1
Region{0} Region Points={1},{2};'''.format(label, point[0], point[1])
        
        label = label + 1
        
        rfile.write(REGION)
    
    rfile.write('\n')
    rfile.close()


if __name__ == '__main__':
  print "Creating regions file..."
  main()