def get_fft_filter(image_shape, min_feature, max_feature, microns_per_pixel):
fftw_hints = pathlib.Path(__file__).parent / 'fftw_hints'
if fftw_hints.exists():
fast_fft.load_plan_hints(str(fftw_hints))
fft_filter = fast_fft.SpatialFilter(image_shape, period_range=(min_feature, max_feature),
spacing=microns_per_pixel, order=2, keep_dc=False, threads=1, better_plan=True)
fast_fft.store_plan_hints(str(fftw_hints))
return fft_filter
import sqlite3
import sys
import time
DPATHSTR = {
'darwin' : '/Volumes/bulkdata/Sinha_Drew/2015.11.13_ZPL8Prelim3'
}.get(sys.platform, '/mnt/bulkdata/Sinha_Drew/2015.11.13_ZPL8Prelim3')
DPATH = Path(DPATHSTR)
from rpc_acquisition.scope.device.autofocus import MultiBrenner
import os.path
from zplib.image import fast_fft
FFTW_WISDOM = os.path.expanduser('~/fftw_wisdom')
if os.path.exists(FFTW_WISDOM):
fast_fft.load_plan_hints(FFTW_WISDOM)
class AutofocusMetric:
def __init__(self, shape):
pass
def metric(self, image):
raise NotImplementedError()
class Brenner(AutofocusMetric):
def metric(self, image):
image = image.astype(numpy.float32) # otherwise can get overflow in the squaring and summation
xd = image.astype(numpy.float32)
yd = image.astype(numpy.float32)
x_diffs = (image[2:, :] - image[:-2, :])**2
xd[1:-1, :] = x_diffs
import freeimage
from zplib.image import fast_fft
from ..util import transfer_ism_buffer
from ..util import logging
from ..config import scope_configuration
from . import andor
from .leica import stage
from . import iotool
logger = logging.get_logger(__name__)
FFTW_WISDOM = scope_configuration.CONFIG_DIR / 'fftw_wisdom'
if FFTW_WISDOM.exists():
loaded = fast_fft.load_plan_hints(str(FFTW_WISDOM))
if loaded:
logger.debug('FFTW wisdom loaded')
else:
logger.warning('FFTW wisdom file exists, but some wisdom could not be loaded (FFTW version mismatch?)')
else:
logger.warning('No FFTW wisdom found!')
@functools.lru_cache(maxsize=16)
def _get_filter(shape, period_range):
timer = threading.Timer(1, logger.warning, ['Slow construction of FFTW filter for image shape {} (likely no cached plan could be found). May take >30 minutes!', shape])
timer.start()
fft_filter = fast_fft.SpatialFilter(shape, period_range, precision=32, threads=6, better_plan=True)
if timer.is_alive():
timer.cancel()
else: # timer went off and warning was issued...
import freeimage
from zplib.image import fast_fft
from ..util import transfer_ism_buffer
from ..util import logging
from ..config import scope_configuration
from . import andor
from .leica import stage
from . import iotool
logger = logging.get_logger(__name__)
FFTW_WISDOM = scope_configuration.CONFIG_DIR / 'fftw_wisdom'
if FFTW_WISDOM.exists():
loaded = fast_fft.load_plan_hints(str(FFTW_WISDOM))
if loaded:
logger.debug('FFTW wisdom loaded')
else:
logger.warning('FFTW wisdom file exists, but some wisdom could not be loaded (FFTW version mismatch?)')
else:
logger.warning('No FFTW wisdom found!')
@functools.lru_cache(maxsize=16)
def _get_filter(shape, period_range):
timer = threading.Timer(1, logger.warning, ['Slow construction of FFTW filter for image shape {} (likely no cached plan could be found). May take >30 minutes!', shape])
timer.start()
fft_filter = fast_fft.SpatialFilter(shape, period_range, precision=32, threads=6, better_plan=True)
if timer.is_alive():
timer.cancel()
else: # timer went off and warning was issued...
