def setUpClass(cls):
path_images = path_image_samples / "Oseen/Images"
series = SeriesOfArrays(str(path_images / "Oseen*"), "i+1:i+3")
cls.path_tmp = path_images.parent / "tmp_test_work_piv"
if not cls.path_tmp.exists():
cls.path_tmp.mkdir()
cls.serie = series.get_serie_from_index(0)
def _make_partition(self, serie_arrays, n):
"""
Partition a SerieOfArrayFromFile into n SeriesOfArray
:param serie_arrays: A SerieOfArrayFromFile
:type SerieOfArrayFromFile
:param n: The number of slices
:type int
:return:
"""
print("nb process = " + str(n))
ind_start = self.params.series.ind_start
ind_stop = self.params.series.ind_stop
ind_step = self.params.series.ind_step
nb_image = ind_stop - ind_start + 1
cut = int(nb_image / n)
rest = nb_image % n
for i in range(n):
if rest > 0:
plus = 1
else:
plus = 0
self.series.append(
SeriesOfArrays(
serie_arrays,
self.params.series.strcouple,
ind_start=ind_start,
ind_stop=ind_start + cut + plus,
ind_step=ind_step,
))
ind_start = ind_start + cut + plus
rest -= 1
from fluidimage import SeriesOfArrays from fluidimage.works.piv import WorkPIV params = WorkPIV.create_default_params() params.multipass.number = 2 params.multipass.use_tps = True params.piv0.shape_crop_im0 = 32 params.piv0.displacement_max = 5 params.fix.correl_min = 0.2 params.fix.threshold_diff_neighbour = 8 params.mask.strcrop = '30:250, 100:' work = WorkPIV(params=params) path = '../../image_samples/Oseen/Images' # path = '../../image_samples/Karman/Images' series = SeriesOfArrays(path, 'i+1:i+3') serie = series.get_serie_from_index(0) piv = work.calcul(serie) # piv.display(show_interp=True, scale=0.3, show_error=True) piv.display(show_interp=False, scale=1, show_error=True) # result.save()
from fluidimage import SeriesOfArrays
from fluidimage.works.piv import WorkPIV
from path_images import get_path
path = os.path.join(get_path('2005C'), 'c*.bmp')
params = WorkPIV.create_default_params()
params.piv0.shape_crop_im0 = 64
params.piv0.grid.overlap = 0.5
params.multipass.number = 3
params.multipass.use_tps = False
params.fix.displacement_max = 3
params.fix.correl_min = 0.1
params.fix.threshold_diff_neighbour = 3
work = WorkPIV(params=params)
series = SeriesOfArrays(path, 'i, 0:2')
serie = series.get_serie_from_index(50)
t0 = time()
piv = work.calcul(serie)
t1 = time()
print('Work done in {:.3f} s.'.format(t1 - t0))
piv.display(show_interp=False, scale=0.1, show_error=True)
from fluidimage import SeriesOfArrays
from fluidimage.works.piv import WorkPIV
params = WorkPIV.create_default_params()
# for a very short computation
params.piv0.shape_crop_im0 = 32
params.piv0.grid.overlap = 0.5
# params.piv0.method_subpix = 'centroid'
# params.piv0.method_correl = 'theano'
params.multipass.number = 2
params.multipass.use_tps = 'last'
params.multipass.coeff_zoom = [2]
piv = WorkPIV(params=params)
series = SeriesOfArrays('../../image_samples/Oseen/Images', 'i+1:i+3')
serie = series.get_serie_from_index(0)
cProfile.runctx('result = piv.calcul(serie)', globals(), locals(),
'profile.pstats')
s = pstats.Stats('profile.pstats')
s.strip_dirs().sort_stats('time').print_stats(10)
print('with gprof2dot and graphviz (command dot):\n'
'gprof2dot -f pstats profile.pstats | dot -Tpng -o profile.png')
class TopologyPIV(TopologyBase):
"""Topology for PIV computation.
The most useful methods for the user (in particular :func:`compute`) are
defined in the base class :class:`fluidimage.topologies.base.TopologyBase`.
Parameters
----------
params : None
A ParamContainer (created with the class method
:func:`create_default_params`) containing the parameters for the
computation.
logging_level : str, {'warning', 'info', 'debug', ...}
Logging level.
nb_max_workers : None, int
Maximum numbers of "workers". If None, a number is estimated from the
number of cores detected. If there are memory errors, you can try to
decrease the number of workers.
"""
@classmethod
def create_default_params(cls):
"""Class method returning the default parameters.
Typical usage::
params = TopologyPIV.create_default_params()
# modify parameters here
...
topo = TopologyPIV(params)
"""
params = ParamContainer(tag="params")
params._set_child(
"series",
attribs={
"path": "",
"strcouple": "i:i+2",
"ind_start": 0,
"ind_stop": None,
"ind_step": 1,
},
)
params.series._set_doc("""
Parameters indicating the input series of images.
path : str, {''}
String indicating the input images (can be a full path towards an image
file or a string given to `glob`).
strcouple : 'i:i+2'
String indicating as a Python slicing how couples of images are formed.
There is one couple per value of `i`. The values of `i` are set with the
other parameters `ind_start`, `ind_step` and `ind_stop` approximately with
the function range (`range(ind_start, ind_stop, ind_step)`).
Python slicing is a very powerful notation to define subset from a
(possibly multidimensional) set of images. For a user, an alternative is to
understand how Python slicing works. See for example this page:
http://stackoverflow.com/questions/509211/explain-pythons-slice-notation.
Another possibility is to follow simple examples:
For single-frame images (im0, im1, im2, im3, ...), we keep the default
value 'i:i+2' to form the couples (im0, im1), (im1, im2), ...
To see what it gives, one can use IPython and range:
>>> i = 0
>>> list(range(10))[i:i+2]
[0, 1]
>>> list(range(10))[i:i+4:2]
[0, 2]
We see that we can also use the value 'i:i+4:2' to form the couples (im0,
im2), (im1, im3), ...
For double-frame images (im1a, im1b, im2a, im2b, ...) you can write
>>> params.series.strcouple = 'i, 0:2'
In this case, the first couple will be (im1a, im1b).
To get the first couple (im1a, im1a), we would have to write
>>> params.series.strcouple = 'i:i+2, 0'
ind_start : int, {0}
ind_step : int, {1}
int_stop : None
""")
params._set_child("saving",
attribs={
"path": None,
"how": "ask",
"postfix": "piv"
})
params.saving._set_doc("""Saving of the results.
path : None or str
Path of the directory where the data will be saved. If None, the path is
obtained from the input path and the parameter `postfix`.
how : str {'ask'}
'ask', 'new_dir', 'complete' or 'recompute'.
postfix : str
Postfix from which the output file is computed.
""")
WorkPIV._complete_params_with_default(params)
params._set_internal_attr(
"_value_text",
json.dumps({
"program": "fluidimage",
"module": "fluidimage.topologies.piv",
"class": "TopologyPIV",
}),
)
params._set_child("preproc")
image2image.complete_im2im_params_with_default(params.preproc)
return params
def __init__(self, params, logging_level="info", nb_max_workers=None):
self.params = params
self.series = SeriesOfArrays(
params.series.path,
params.series.strcouple,
ind_start=params.series.ind_start,
ind_stop=params.series.ind_stop,
ind_step=params.series.ind_step,
)
path_dir = self.series.serie.path_dir
path_dir_result, self.how_saving = prepare_path_dir_result(
path_dir, params.saving.path, params.saving.postfix,
params.saving.how)
super().__init__(
path_dir_result=path_dir_result,
logging_level=logging_level,
nb_max_workers=nb_max_workers,
)
queue_couples_of_names = self.add_queue("couples of names")
queue_paths = self.add_queue("paths")
queue_arrays = queue_arrays1 = self.add_queue("arrays")
queue_couples_of_arrays = self.add_queue("couples of arrays")
queue_piv = self.add_queue("piv")
if params.preproc.im2im is not None:
queue_arrays1 = self.add_queue("arrays1")
self.add_work(
"fill (couples of names, paths)",
func_or_cls=self.fill_couples_of_names_and_paths,
output_queue=(queue_couples_of_names, queue_paths),
kind=("global", "one shot"),
)
self.add_work(
"read array",
func_or_cls=imread,
input_queue=queue_paths,
output_queue=queue_arrays,
kind="io",
)
if params.preproc.im2im is not None:
im2im_func = image2image.TopologyImage2Image.init_im2im(
self, params.preproc)
self.add_work(
"image2image",
func_or_cls=im2im_func,
input_queue=queue_arrays,
output_queue=queue_arrays1,
)
self.add_work(
"make couples of arrays",
func_or_cls=self.make_couples,
params_cls=None,
input_queue=(queue_couples_of_names, queue_arrays),
output_queue=queue_couples_of_arrays,
kind="global",
)
self.work_piv = WorkPIV(self.params)
self.add_work(
"compute piv",
func_or_cls=self.work_piv.calcul,
params_cls=params,
input_queue=queue_couples_of_arrays,
output_queue=queue_piv,
)
self.add_work(
"save piv",
func_or_cls=self.save_piv_object,
input_queue=queue_piv,
kind="io",
)
self.results = []
def save_piv_object(self, obj):
"""Save a PIV object"""
ret = obj.save(self.path_dir_result)
self.results.append(ret)
def fill_couples_of_names_and_paths(self, input_queue, output_queues):
"""Fill the two first queues"""
assert input_queue is None
queue_couples_of_names = output_queues[0]
queue_paths = output_queues[1]
series = self.series
if not series:
logger.warning("add 0 couple. No PIV to compute.")
return
if self.how_saving == "complete":
index_series = []
for ind_serie, serie in self.series.items():
name_piv = get_name_piv(serie, prefix="piv")
if not (self.path_dir_result / name_piv).exists():
index_series.append(ind_serie)
if not index_series:
logger.warning(
'topology in mode "complete" and work already done.')
return
series.set_index_series(index_series)
if logger.isEnabledFor(DEBUG):
logger.debug(
repr([serie.get_name_arrays() for serie in series]))
nb_series = len(series)
logger.info(f"Add {nb_series} PIV fields to compute.")
for iserie, serie in enumerate(series):
if iserie > 1:
break
logger.info("Files of serie {}: {}".format(
iserie, serie.get_name_arrays()))
for ind_serie, serie in series.items():
queue_couples_of_names[ind_serie] = serie.get_name_arrays()
for name, path in serie.get_name_path_arrays():
queue_paths[name] = path
def make_couples(self, input_queues, output_queue):
"""Make the couples of arrays"""
queue_couples_of_names = input_queues[0]
queue_arrays = input_queues[1]
try:
params_mask = self.params.mask
except AttributeError:
params_mask = None
# for each name couple
for key, couple in tuple(queue_couples_of_names.items()):
# if correspondant arrays are available, make an array couple
if (couple[0] in queue_arrays.keys()
and couple[1] in queue_arrays.keys()):
array1 = queue_arrays[couple[0]]
array2 = queue_arrays[couple[1]]
serie = copy.copy(self.series.get_serie_from_index(key))
# logger.debug(
# f"create couple {key}: {couple}, ({array1}, {array2})"
# )
array_couple = ArrayCouple(
names=(couple[0], couple[1]),
arrays=(array1, array2),
params_mask=params_mask,
serie=serie,
)
output_queue[key] = array_couple
del queue_couples_of_names[key]
# remove the image_array if it not will be used anymore
if not is_name_in_queue(couple[0], queue_couples_of_names):
del queue_arrays[couple[0]]
if not is_name_in_queue(couple[1], queue_couples_of_names):
del queue_arrays[couple[1]]
def make_text_at_exit(self, time_since_start):
"""Make a text printed at exit"""
txt = f"Stop compute after t = {time_since_start:.2f} s"
try:
nb_results = len(self.results)
except AttributeError:
nb_results = None
if nb_results is not None and nb_results > 0:
txt += f" ({nb_results} piv fields, {time_since_start / nb_results:.2f} s/field)."
else:
txt += "."
txt += "\npath results:\n" + str(self.path_dir_result)
return txt
def __init__(self, params, logging_level="info", nb_max_workers=None):
self.params = params
self.series = SeriesOfArrays(
params.series.path,
params.series.strcouple,
ind_start=params.series.ind_start,
ind_stop=params.series.ind_stop,
ind_step=params.series.ind_step,
)
path_dir = self.series.serie.path_dir
path_dir_result, self.how_saving = prepare_path_dir_result(
path_dir, params.saving.path, params.saving.postfix,
params.saving.how)
super().__init__(
path_dir_result=path_dir_result,
logging_level=logging_level,
nb_max_workers=nb_max_workers,
)
queue_couples_of_names = self.add_queue("couples of names")
queue_paths = self.add_queue("paths")
queue_arrays = queue_arrays1 = self.add_queue("arrays")
queue_couples_of_arrays = self.add_queue("couples of arrays")
queue_piv = self.add_queue("piv")
if params.preproc.im2im is not None:
queue_arrays1 = self.add_queue("arrays1")
self.add_work(
"fill (couples of names, paths)",
func_or_cls=self.fill_couples_of_names_and_paths,
output_queue=(queue_couples_of_names, queue_paths),
kind=("global", "one shot"),
)
self.add_work(
"read array",
func_or_cls=imread,
input_queue=queue_paths,
output_queue=queue_arrays,
kind="io",
)
if params.preproc.im2im is not None:
im2im_func = image2image.TopologyImage2Image.init_im2im(
self, params.preproc)
self.add_work(
"image2image",
func_or_cls=im2im_func,
input_queue=queue_arrays,
output_queue=queue_arrays1,
)
self.add_work(
"make couples of arrays",
func_or_cls=self.make_couples,
params_cls=None,
input_queue=(queue_couples_of_names, queue_arrays),
output_queue=queue_couples_of_arrays,
kind="global",
)
self.work_piv = WorkPIV(self.params)
self.add_work(
"compute piv",
func_or_cls=self.work_piv.calcul,
params_cls=params,
input_queue=queue_couples_of_arrays,
output_queue=queue_piv,
)
self.add_work(
"save piv",
func_or_cls=self.save_piv_object,
input_queue=queue_piv,
kind="io",
)
self.results = []
def __init__(self, params, logging_level="info", nb_max_workers=None):
self.params = params
if params.surface_tracking is None:
raise ValueError("params.surface_tracking has to be set.")
self.serie = SerieOfArraysFromFiles(params.images.path,
params.images.str_slice)
self.series = SeriesOfArrays(
params.images.path,
"i:i+" + str(self.serie.get_index_slices()[0][2] + 1) + ":" +
str(self.serie.get_index_slices()[0][2]),
ind_start=self.serie.get_index_slices()[0][0],
ind_stop=self.serie.get_index_slices()[0][1] - 1,
ind_step=self.serie.get_index_slices()[0][2],
)
path_dir = self.serie.path_dir
path_dir_result, self.how_saving = prepare_path_dir_result(
path_dir, params.saving.path, params.saving.postfix,
params.saving.how)
self.path_dir_result = path_dir_result
self.path_dir_src = Path(path_dir)
self.surface_tracking_work = WorkSurfaceTracking(params)
super().__init__(
path_dir_result=path_dir_result,
logging_level=logging_level,
nb_max_workers=nb_max_workers,
)
queue_paths = self.add_queue("paths")
queue_couples_of_names = self.add_queue("couples of names")
queue_arrays = self.add_queue("arrays")
queue_angles = self.add_queue("angles")
queue_couples_of_arrays = self.add_queue(
"couples of corrected angles and angles")
queuemod0_angles = self.add_queue("corrected angles copy")
queuemod_angles = self.add_queue("corrected angles")
queue_heights = self.add_queue("heights")
self.add_work(
"fill_path",
self.fill_queue_paths,
output_queue=(queue_paths, queue_couples_of_names),
kind="one shot",
)
self.add_work(
"read_array",
self.imread,
input_queue=queue_paths,
output_queue=queue_arrays,
kind="io",
)
self.add_work(
"process_frame",
self.surface_tracking_work.process_frame_func,
input_queue=queue_arrays,
output_queue=queue_angles,
)
self.add_work(
"create_couple",
self.make_couples,
input_queue=(queuemod0_angles, queue_angles,
queue_couples_of_names),
output_queue=(queuemod_angles, queue_couples_of_arrays),
kind="global",
)
self.add_work(
"correct_couple_of_phases",
self.surface_tracking_work.correctcouple,
input_queue=queue_couples_of_arrays,
output_queue=queuemod0_angles,
)
self.add_work(
"calcul_height",
self.surface_tracking_work.calculheight_func,
input_queue=queuemod_angles,
output_queue=queue_heights,
)
self.add_work("save",
self.save_image,
input_queue=queue_heights,
kind="io")
class TopologyBOS(TopologyBase):
"""Topology for BOS.
See https://en.wikipedia.org/wiki/Background-oriented_schlieren_technique
Parameters
----------
params : None
A ParamContainer containing the parameters for the computation.
logging_level : str, {'warning', 'info', 'debug', ...}
Logging level.
nb_max_workers : None, int
Maximum numbers of "workers". If None, a number is computed from the
number of cores detected. If there are memory errors, you can try to
decrease the number of workers.
"""
@classmethod
def create_default_params(cls):
"""Class method returning the default parameters.
For developers: cf. fluidsim.base.params
"""
params = ParamContainer(tag="params")
params._set_attrib("reference", 0)
params._set_doc("""
reference : str or int, {0}
Reference file (from which the displacements will be computed). Can be an
absolute file path, a file name or the index in the list of files found
from the parameters in ``params.series``.
""")
params._set_child(
"series",
attribs={
"path": "",
"strslice": None,
"ind_start": 0,
"ind_stop": None,
"ind_step": 1,
},
)
params.series._set_doc("""
Parameters indicating the input series of images.
path : str, {''}
String indicating the input images (can be a full path towards an image
file or a string given to `glob`).
strslice : None
String indicating as a Python slicing how series of images are formed.
See the parameters the PIV topology.
ind_start : int, {0}
ind_step : int, {1}
int_stop : None
""")
params._set_child("saving",
attribs={
"path": None,
"how": "ask",
"postfix": "piv"
})
params.saving._set_doc("""Saving of the results.
path : None or str
Path of the directory where the data will be saved. If None, the path is
obtained from the input path and the parameter `postfix`.
how : str {'ask'}
'ask', 'new_dir', 'complete' or 'recompute'.
postfix : str
Postfix from which the output file is computed.
""")
WorkPIV._complete_params_with_default(params)
params._set_internal_attr(
"_value_text",
json.dumps({
"program": "fluidimage",
"module": "fluidimage.topologies.bos",
"class": "TopologyBOS",
}),
)
return params
def __init__(self, params=None, logging_level="info", nb_max_workers=None):
if params is None:
params = self.__class__.create_default_params()
self.params = params
self.piv_work = WorkPIV(params)
self.series = SeriesOfArrays(
params.series.path,
params.series.strslice,
ind_start=params.series.ind_start,
ind_stop=params.series.ind_stop,
ind_step=params.series.ind_step,
)
path_dir = self.series.serie.path_dir
path_dir_result, self.how_saving = prepare_path_dir_result(
path_dir, params.saving.path, params.saving.postfix,
params.saving.how)
self.path_dir_result = path_dir_result
if not isinstance(params.reference, int):
reference = os.path.expanduser(params.reference)
else:
reference = params.reference
if isinstance(reference, int):
names = self.series.get_name_all_arrays()
names.sort()
path_reference = os.path.join(path_dir, names[reference])
elif os.path.isfile(reference):
path_reference = reference
else:
path_reference = os.path.join(path_dir_result, reference)
if not os.path.isfile(path_reference):
raise ValueError("Bad value of params.reference:" +
path_reference)
self.path_reference = path_reference
self.image_reference = imread(path_reference)
self.results = {}
def save_piv_object(o):
ret = o.save(path_dir_result, kind="bos")
return ret
self.wq_piv = WaitingQueueThreading("delta",
save_piv_object,
self.results,
topology=self)
self.wq_couples = WaitingQueueMultiprocessing("couple",
self.piv_work.calcul,
self.wq_piv,
topology=self)
self.wq_images = WaitingQueueMakeCoupleBOS(
"array image",
self.wq_couples,
topology=self,
image_reference=self.image_reference,
path_reference=self.path_reference,
serie=self.series.serie,
)
self.wq0 = WaitingQueueLoadImage(destination=self.wq_images,
path_dir=path_dir,
topology=self)
super().__init__(
[self.wq0, self.wq_images, self.wq_couples, self.wq_piv],
path_output=path_dir_result,
logging_level=logging_level,
nb_max_workers=nb_max_workers,
)
self.add_series(self.series)
def add_series(self, series):
if len(series) == 0:
logger.warning("add 0 image. No BOS to compute.")
return
names = series.get_name_all_arrays()
if self.how_saving == "complete":
names_to_compute = []
for name in names:
name_bos = get_name_bos(name, series.serie)
if not os.path.exists(
os.path.join(self.path_dir_result, name_bos)):
names_to_compute.append(name)
names = names_to_compute
if len(names) == 0:
logger.warning(
'topology in mode "complete" and work already done.')
return
nb_names = len(names)
print("Add {} BOS fields to compute.".format(nb_names))
logger.debug(repr(names))
print("First files to process:", names[:4])
self.wq0.add_name_files(names)
# a little bit strange, to apply mask...
try:
params_mask = self.params.mask
except AttributeError:
params_mask = None
im = self.image_reference
couple = ArrayCouple(names=("", ""),
arrays=(im, im),
params_mask=params_mask)
im, _ = couple.get_arrays()
self.piv_work._prepare_with_image(im)
def print_at_exit(self, time_since_start):
txt = "Stop compute after t = {:.2f} s".format(time_since_start)
try:
nb_results = len(self.results)
except AttributeError:
nb_results = None
if nb_results is not None and nb_results > 0:
txt += " ({} bos fields, {:.2f} s/field).".format(
nb_results, time_since_start / nb_results)
else:
txt += "."
txt += "\npath results:\n" + str(self.path_dir_result)
print(txt)
def __init__(self, params=None, logging_level="info", nb_max_workers=None):
if params is None:
params = self.__class__.create_default_params()
self.params = params
self.piv_work = WorkPIV(params)
self.series = SeriesOfArrays(
params.series.path,
params.series.strslice,
ind_start=params.series.ind_start,
ind_stop=params.series.ind_stop,
ind_step=params.series.ind_step,
)
path_dir = self.series.serie.path_dir
path_dir_result, self.how_saving = prepare_path_dir_result(
path_dir, params.saving.path, params.saving.postfix,
params.saving.how)
self.path_dir_result = path_dir_result
if not isinstance(params.reference, int):
reference = os.path.expanduser(params.reference)
else:
reference = params.reference
if isinstance(reference, int):
names = self.series.get_name_all_arrays()
names.sort()
path_reference = os.path.join(path_dir, names[reference])
elif os.path.isfile(reference):
path_reference = reference
else:
path_reference = os.path.join(path_dir_result, reference)
if not os.path.isfile(path_reference):
raise ValueError("Bad value of params.reference:" +
path_reference)
self.path_reference = path_reference
self.image_reference = imread(path_reference)
self.results = {}
def save_piv_object(o):
ret = o.save(path_dir_result, kind="bos")
return ret
self.wq_piv = WaitingQueueThreading("delta",
save_piv_object,
self.results,
topology=self)
self.wq_couples = WaitingQueueMultiprocessing("couple",
self.piv_work.calcul,
self.wq_piv,
topology=self)
self.wq_images = WaitingQueueMakeCoupleBOS(
"array image",
self.wq_couples,
topology=self,
image_reference=self.image_reference,
path_reference=self.path_reference,
serie=self.series.serie,
)
self.wq0 = WaitingQueueLoadImage(destination=self.wq_images,
path_dir=path_dir,
topology=self)
super().__init__(
[self.wq0, self.wq_images, self.wq_couples, self.wq_piv],
path_output=path_dir_result,
logging_level=logging_level,
nb_max_workers=nb_max_workers,
)
self.add_series(self.series)
import params_piv
try:
reload
except NameError:
from importlib import reload
reload(params_piv)
iexp = 0
params = params_piv.make_params_piv(iexp)
work = WorkPIV(params=params)
pathin = params.series.path
series = SeriesOfArrays(pathin,
params.series.strcouple,
ind_start=params.series.ind_start)
# c060a.png and c060b.png
serie = series.get_serie_from_index(params.series.ind_start)
piv = work.calcul(serie)
# piv.piv0.display(show_interp=True, scale=0.05, show_error=True)
piv.display(show_interp=False, scale=0.05, show_error=True)
def __init__(self, params=None, logging_level="info", nb_max_workers=None):
if params is None:
params = self.__class__.create_default_params()
self.params = params
self.piv_work = WorkPIV(params)
serie_arrays = SerieOfArraysFromFiles(params.series.path)
self.series = SeriesOfArrays(
serie_arrays,
params.series.strcouple,
ind_start=params.series.ind_start,
ind_stop=params.series.ind_stop,
ind_step=params.series.ind_step,
)
path_dir = self.series.serie.path_dir
path_dir_result, self.how_saving = prepare_path_dir_result(
path_dir, params.saving.path, params.saving.postfix,
params.saving.how)
self.path_dir_result = path_dir_result
self.results = {}
def save_piv_object(o):
ret = o.save(path_dir_result)
return ret
self.wq_piv = WaitingQueueThreading("delta",
save_piv_object,
self.results,
topology=self)
self.wq_couples = WaitingQueueMultiprocessing("couple",
self.piv_work.calcul,
self.wq_piv,
topology=self)
self.wq_images = WaitingQueueMakeCouple("array image",
self.wq_couples,
topology=self)
if params.preproc.im2im is not None:
self.im2im_func = image2image.TopologyImage2Image.init_im2im(
self, params.preproc)
self.wq_images0 = WaitingQueueMultiprocessing("image ",
self.im2im_func,
self.wq_images,
topology=self)
wq_after_load = self.wq_images0
else:
wq_after_load = self.wq_images
self.wq0 = WaitingQueueLoadImage(destination=wq_after_load,
path_dir=path_dir,
topology=self)
if params.preproc.im2im is not None:
waiting_queues = [
self.wq0,
self.wq_images0,
self.wq_images,
self.wq_couples,
self.wq_piv,
]
else:
waiting_queues = [
self.wq0,
self.wq_images,
self.wq_couples,
self.wq_piv,
]
super().__init__(
waiting_queues,
path_output=path_dir_result,
logging_level=logging_level,
nb_max_workers=nb_max_workers,
)
self.add_series(self.series)
# params.piv0.method_correl = 'pythran'
params.multipass.number = 1
params.multipass.use_tps = False
# params.multipass.coeff_zoom = [2, 2]
# bug params.piv0.shape_crop_im0 = 128 # !!
params.piv0.shape_crop_im0 = 64 # (80, 90)
# params.piv0.shape_crop_im1 = (38, 36)
params.fix.correl_min = 0.2
params.fix.threshold_diff_neighbour = 4
# params.piv0.grid.overlap = 10
piv = WorkPIV(params=params)
series = SeriesOfArrays("../../../image_samples/Oseen/Images", "i+1:i+3")
serie = series.get_serie_from_index(0)
result = piv.calcul(serie)
result.display()
result.save()
# lightresult = result.make_light_result()
# lightresult.save()
# lightresultload = LightPIVResults(str_path='piv_Oseen_center01-02_light.h5')
# f=h5netcdf.File('piv_Oseen_center01-02.h5')
# f=h5py.File('piv_Oseen_center01-02.h5')
class TopologyPreproc(TopologyBase):
"""Preprocess series of images.
The most useful methods for the user (in particular :func:`compute`) are
defined in the base class :class:`fluidimage.topologies.base.TopologyBase`.
Parameters
----------
params: None
A ParamContainer (created with the class method
:func:`create_default_params`) containing the parameters for the
computation.
logging_level: str, {'warning', 'info', 'debug', ...}
Logging level.
nb_max_workers: None, int
Maximum numbers of "workers". If None, a number is computed from the
number of cores detected. If there are memory errors, you can try to
decrease the number of workers.
"""
@classmethod
def create_default_params(cls, backend="python"):
"""Class method returning the default parameters.
Typical usage::
params = TopologyPreproc.create_default_params()
# modify parameters here
...
topo = TopologyPreproc(params)
Parameters
----------
backend : {'python', 'opencv'}
Specifies which backend to use.
"""
params = WorkPreproc.create_default_params(backend)
params.preproc.series._set_attribs({
"strcouple": "i:i+1",
"ind_start": 0,
"ind_stop": None,
"ind_step": 1,
})
params.preproc.series._set_doc("""
Parameters describing image loading prior to preprocessing.
strcouple : str
Determines the subset from the whole series of images that should be loaded
and preprocessed together. Particularly useful when temporal filtering requires
multiple images.
For example, for a series of images with just one index,
>>> strcouple = 'i:i+1' # load one image at a time
>>> strcouple = 'i-2:i+3' # loads 5 images at a time
Similarly for two indices,
>>> strcouple = 'i:i+1,0' # load one image at a time, with second index fixed
>>> strcouple = 'i-2:i+3,0' # loads 5 images at a time, with second index fixed
.. todo::
Rename this parameter to strsubset / strslice
ind_start : int
Start index for the whole series of images being loaded.
For more details: see `class SeriesOfArrays`.
ind_stop : int
Stop index for the whole series of images being loaded.
For more details: see `class SeriesOfArrays`.
ind_step : int
Step index for the whole series of images being loaded.
For more details: see `class SeriesOfArrays`.
""")
params.preproc._set_child(
"saving",
attribs={
"path": None,
"strcouple": None,
"how": "ask",
"format": "img",
"postfix": "pre",
},
)
params.preproc.saving._set_doc("""
Parameters describing image saving after preprocessing.
path : str or None
Path to which preprocessed images are saved.
str_subset : str or None
NotImplemented! Determines the sub-subset of images must be saved from subset
of images that were loaded and preprocessed. When set as None, saves the
middle image from every subset.
.. todo::
Implement the option params.saving.str_subset...
how : str {'ask', 'new_dir', 'complete', 'recompute'}
How preprocessed images must be saved if it already exists or not.
format : str {'img', 'hdf5'}
Format in which preprocessed image data must be saved.
postfix : str
A suffix added to the new directory where preprocessed images are saved.
""")
params._set_internal_attr(
"_value_text",
json.dumps({
"program": "fluidimage",
"module": "fluidimage.topologies.preproc",
"class": "TopologyPreproc",
}),
)
params._set_child("im2im")
image2image.complete_im2im_params_with_default(params.im2im)
return params
def __init__(self,
params: ParamContainer,
logging_level="info",
nb_max_workers=None):
self.params = params.preproc
self.preproc_work = WorkPreproc(params)
self.results = []
self.display = self.preproc_work.display
serie_arrays = self.preproc_work.serie_arrays
self.series = SeriesOfArrays(
serie_arrays,
params.preproc.series.strcouple,
ind_start=params.preproc.series.ind_start,
ind_stop=params.preproc.series.ind_stop,
ind_step=params.preproc.series.ind_step,
)
subset = self.series.get_serie_from_index(0)
self.nb_items_per_serie = subset.get_nb_arrays()
if os.path.isdir(params.preproc.series.path):
path_dir = params.preproc.series.path
else:
path_dir = os.path.dirname(params.preproc.series.path)
self.path_dir_input = path_dir
path_dir_result, self.how_saving = prepare_path_dir_result(
path_dir,
params.preproc.saving.path,
params.preproc.saving.postfix,
params.preproc.saving.how,
)
super().__init__(
path_dir_result=path_dir_result,
logging_level=logging_level,
nb_max_workers=nb_max_workers,
)
self.params.saving.path = self.path_dir_result
# Define waiting queues
queue_subsets_of_names = self.add_queue("subsets of filenames")
queue_paths = self.add_queue("image paths")
queue_arrays = queue_arrays1 = self.add_queue("arrays")
queue_subsets_of_arrays = self.add_queue("subsets of arrays")
queue_preproc_objects = self.add_queue("preproc results")
if params.im2im.im2im is not None:
queue_arrays1 = self.add_queue("arrays1")
# Define works
self.add_work(
"fill (subsets_of_names, paths)",
func_or_cls=self.fill_subsets_of_names_and_paths,
output_queue=(queue_subsets_of_names, queue_paths),
kind=("global", "one shot"),
)
self.add_work(
"imread",
func_or_cls=imread,
input_queue=queue_paths,
output_queue=queue_arrays,
kind="io",
)
if params.im2im.im2im is not None:
im2im_func = image2image.TopologyImage2Image.init_im2im(
self, params.im2im)
self.add_work(
"image2image",
func_or_cls=im2im_func,
input_queue=queue_arrays,
output_queue=queue_arrays1,
)
self.add_work(
"make subsets of arrays",
func_or_cls=self.make_subsets,
input_queue=(queue_subsets_of_names, queue_arrays1),
output_queue=queue_subsets_of_arrays,
kind="global",
)
self.add_work(
"preproc a subset of arrays",
func_or_cls=self.preproc_work.calcul,
params_cls=params,
input_queue=queue_subsets_of_arrays,
output_queue=queue_preproc_objects,
)
self.add_work(
"save images",
func_or_cls=self.save_preproc_object,
input_queue=queue_preproc_objects,
kind="io",
)
def save_preproc_object(self, obj: ArraySubset):
"""Save a preprocessing object"""
ret = obj.save(path=self.path_dir_result)
self.results.append(ret)
def init_series(self) -> List[str]:
"""Initializes the SeriesOfArrays object `self.series` based on input
parameters."""
series = self.series
if not series:
logger.warning(
"encountered empty series. No images to preprocess.")
return
if self.how_saving == "complete":
index_subsets = []
for ind_subset, subset in self.series.items():
names_serie = subset.get_name_arrays()
name_preproc = get_name_preproc(
subset,
names_serie,
ind_subset,
series.nb_series,
self.params.saving.format,
)
if not (self.path_dir_result / name_preproc).exists():
index_subsets.append(ind_subset)
series.set_index_series(index_subsets)
if logger.isEnabledFor(DEBUG):
logger.debug(
repr([subset.get_name_arrays() for subset in series]))
nb_subsets = len(series)
if nb_subsets == 0:
logger.warning(
'topology in mode "complete" and work already done.')
return
elif nb_subsets == 1:
plurial = ""
else:
plurial = "s"
logger.info(f"Add {nb_subsets} image serie{plurial} to compute.")
def fill_subsets_of_names_and_paths(self, input_queue: None,
output_queues: Tuple[Dict]) -> None:
"""Fill the two first queues"""
assert input_queue is None
queue_subsets_of_names, queue_paths = output_queues
self.init_series()
for ind_subset, subset in self.series.items():
queue_subsets_of_names[ind_subset] = subset.get_name_arrays()
for name, path in subset.get_name_path_arrays():
queue_paths[name] = path
def make_subsets(self, input_queues: Tuple[Dict],
output_queue: Dict) -> bool:
"""Create the subsets of images"""
queue_subsets_of_names, queue_arrays = input_queues
# for each name subset
for key, names in list(queue_subsets_of_names.items()):
# if correspondant arrays have been loaded from images,
# make an array subset
if all([name in queue_arrays for name in names]):
arrays = (queue_arrays[name] for name in names)
serie = copy.copy(self.series.get_serie_from_index(key))
array_subset = ArraySubset(names=names,
arrays=arrays,
serie=serie)
output_queue[key] = array_subset
del queue_subsets_of_names[key]
# remove the image_array if it not will be used anymore
key_arrays = list(queue_arrays.keys())
for key_array in key_arrays:
if not is_name_in_queue(key_array, queue_subsets_of_names):
del queue_arrays[key_array]
def __init__(self,
params: ParamContainer,
logging_level="info",
nb_max_workers=None):
self.params = params.preproc
self.preproc_work = WorkPreproc(params)
self.results = []
self.display = self.preproc_work.display
serie_arrays = self.preproc_work.serie_arrays
self.series = SeriesOfArrays(
serie_arrays,
params.preproc.series.strcouple,
ind_start=params.preproc.series.ind_start,
ind_stop=params.preproc.series.ind_stop,
ind_step=params.preproc.series.ind_step,
)
subset = self.series.get_serie_from_index(0)
self.nb_items_per_serie = subset.get_nb_arrays()
if os.path.isdir(params.preproc.series.path):
path_dir = params.preproc.series.path
else:
path_dir = os.path.dirname(params.preproc.series.path)
self.path_dir_input = path_dir
path_dir_result, self.how_saving = prepare_path_dir_result(
path_dir,
params.preproc.saving.path,
params.preproc.saving.postfix,
params.preproc.saving.how,
)
super().__init__(
path_dir_result=path_dir_result,
logging_level=logging_level,
nb_max_workers=nb_max_workers,
)
self.params.saving.path = self.path_dir_result
# Define waiting queues
queue_subsets_of_names = self.add_queue("subsets of filenames")
queue_paths = self.add_queue("image paths")
queue_arrays = queue_arrays1 = self.add_queue("arrays")
queue_subsets_of_arrays = self.add_queue("subsets of arrays")
queue_preproc_objects = self.add_queue("preproc results")
if params.im2im.im2im is not None:
queue_arrays1 = self.add_queue("arrays1")
# Define works
self.add_work(
"fill (subsets_of_names, paths)",
func_or_cls=self.fill_subsets_of_names_and_paths,
output_queue=(queue_subsets_of_names, queue_paths),
kind=("global", "one shot"),
)
self.add_work(
"imread",
func_or_cls=imread,
input_queue=queue_paths,
output_queue=queue_arrays,
kind="io",
)
if params.im2im.im2im is not None:
im2im_func = image2image.TopologyImage2Image.init_im2im(
self, params.im2im)
self.add_work(
"image2image",
func_or_cls=im2im_func,
input_queue=queue_arrays,
output_queue=queue_arrays1,
)
self.add_work(
"make subsets of arrays",
func_or_cls=self.make_subsets,
input_queue=(queue_subsets_of_names, queue_arrays1),
output_queue=queue_subsets_of_arrays,
kind="global",
)
self.add_work(
"preproc a subset of arrays",
func_or_cls=self.preproc_work.calcul,
params_cls=params,
input_queue=queue_subsets_of_arrays,
output_queue=queue_preproc_objects,
)
self.add_work(
"save images",
func_or_cls=self.save_preproc_object,
input_queue=queue_preproc_objects,
kind="io",
)
import os
from fluidimage import SeriesOfArrays
from fluidimage.works.piv import WorkPIV
from path_images import get_path
params = WorkPIV.create_default_params()
params.piv0.shape_crop_im0 = 128
params.piv0.grid.overlap = 0.5
params.multipass.number = 2
params.multipass.use_tps = False
params.fix.displacement_max = 15
params.fix.correl_min = 0.1
piv = WorkPIV(params=params)
path = os.path.join(get_path('2001A'), 'A*')
series = SeriesOfArrays(path, 'i, 1:3', ind_start=1)
serie = series.get_serie_from_index(1)
result = piv.calcul(serie)
result.display()