def compare(self, indices=(0, 1), suffix=None, hist=False):
if not suffix:
suffix = "." + self.params.saving.postfix
pathbase = self.params.series.path + "/"
names = self.series.get_name_all_arrays()
im0 = imread(pathbase + names[indices[0]])
im1 = imread(pathbase + names[indices[1]])
im0p = imread(pathbase[:-1] + suffix + "/" + names[indices[0]])
im1p = imread(pathbase[:-1] + suffix + "/" + names[indices[1]])
return DisplayPreProc(im0, im1, im0p, im1p, hist=hist)
def __init__(
self,
point0,
point1,
distance,
aspect_ratio_pixel=1.0,
shape_image=None,
path_image=None,
point_origin=(0, 0),
orig_phys=(0.0, 0.0),
):
self.point0 = np.array(point0)
self.point1 = np.array(point1)
self.distance = distance
delta_point = self.point1 - self.point0
self.aspect_ratio_pixel = aspect_ratio_pixel
self.xphys1pixel = distance / np.sqrt(delta_point[0]**2 +
(aspect_ratio_pixel *
delta_point[1])**2)
self.yphys1pixel = aspect_ratio_pixel * self.xphys1pixel
if shape_image is None:
arr = imread(path_image)
shape_image = arr.shape
self.shape_image = shape_image
self.ix_origin = point_origin[1]
self.iy_origin = point_origin[0]
self.xphys_origin = orig_phys[1]
self.yphys_origin = orig_phys[0]
def setUpClass(cls):
path_in = path_image_samples / cls.name / "Images"
cls._work_dir = Path("test_topo_preproc_" + cls.name) / "Images"
cls._work_dir.mkdir(parents=True, exist_ok=True)
paths = path_in.glob("*")
for path in paths:
name = path.name
im = imread(path)
im = im[::6, ::6]
imsave(str(cls._work_dir / name), im, as_int=True)
def setUpClass(cls):
path_in = str(path_image_samples / cls.name / "Images")
cls._work_dir = os.path.join(
"test_fluidimage_topo_preproc_" + cls.name, "Images")
if not os.path.exists(cls._work_dir):
os.makedirs(cls._work_dir)
paths = glob(path_in + "/*")
for path in paths:
name = os.path.split(path)[-1]
im = imread(path)
im = im[::6, ::6]
imsave(os.path.join(cls._work_dir, name), im, as_int=True)
def loadim(self, ifile, im=None):
_print_debug("loadim", ifile, im)
if im is None:
im = imread(self.path_files[ifile])
_print_debug(self.path_files[ifile])
_print_debug(im)
self.mappable = self.ax.imshow(
im,
interpolation="nearest",
cmap=self.cmap,
origin="upper",
extent=[0, im.shape[1], im.shape[0], 0],
vmin=self.clim[0],
vmax=self.clim[1],
)
self.maps[ifile] = self.mappable
def load(k):
log("load")
return (k, imread(k))
for i0, i1 in center_indices:
ni1 = np.zeros_like(di_range)
ni2 = np.zeros_like(di_range)
for i, di in enumerate(di_range):
di2 = di // 2
slice0 = slice(i0 - di2, i0 + di2)
slice1 = slice(i1 - di2, i1 + di2)
ni1[i] = particle_count(img1[slice0, slice1])
ni2[i] = particle_count(img2[slice0, slice1])
fio = ni2.astype(float) / ni1
ax.plot(di_range, fio, label="centre: {},{}".format(i0, i1))
ax.legend()
plt.show()
if __name__ == "__main__":
import sys
from fluiddyn.io.image import imread
img1 = imread(sys.argv[1])
img2 = imread(sys.argv[2])
argv = map(int, sys.argv[3:])
center_indices = list(zip(argv[0::2], argv[1::2]))
print(sys.argv)
print(center_indices)
particle_density(img1, center_indices)
particle_motion_factor(img1, img2, center_indices)
def __init__(self, args):
if str_error_import_textbox:
raise ImportError(str_error_import_textbox)
path_in = args.path
if os.path.isdir(path_in):
self.path_files = glob(os.path.join(path_in, "*"))
self.path_files = [
path for path in self.path_files if check_image(path)
]
self.path_files.sort()
ifile = 0
else:
path_file = glob(path_in)[0]
self.path_files = glob(os.path.join(os.path.split(path_file)[0], "*"))
self.path_files = [
path for path in self.path_files if check_image(path)
]
self.path_files.sort()
ifile = self.path_files.index(path_file)
if len(self.path_files) == 0:
raise ValueError("No image files detected.")
if len(self.path_files) == 1 and self.path_files[0].endswith(".cine"):
serie = SerieOfArraysFromFiles(self.path_files[0])
self.path_files = serie.get_path_arrays()
path_dir = os.path.split(self.path_files[0])[0]
self.nb_images = len(self.path_files)
print("Will use {} images in the dir {}".format(self.nb_images, path_dir))
self._buttons = {}
self._textboxes = {}
fig = self.fig = plt.figure()
fig.canvas.set_window_title(
path_dir + " (" + time_as_str()[-8:].replace("-", ":") + ")"
)
self.ax = fig.add_axes([0.07, 0.15, 0.7, 0.78])
self.maps = {}
try:
self.cmap = plt.cm.viridis
except AttributeError:
self.cmap = plt.cm.jet
self.ifile = ifile
self._last_was_increase = False
im = imread(self.path_files[ifile])
self.clim = [0, 0.99 * im.max()]
self._updating_clim = False
self.loadim(ifile, im)
name_file = self.get_namefile()
self.ax.set_title(name_file)
self._image_changing = False
function_buttons = [None] * len(name_buttons)
function_buttons[0] = self._decrease_ifile_n
function_buttons[1] = self._decrease_ifile
function_buttons[2] = self._increase_ifile
function_buttons[3] = self._increase_ifile_n
y = size_button / 3.0
for i, x in enumerate(x_buttons):
name = name_buttons[i]
func = function_buttons[i]
self._create_button(fig, [x, y, size_button, size_button], name, func)
self._n = 1
self._create_text(
fig,
[0.1, y, 2 * size_button, size_button],
"n = ",
self._submit_n,
"1",
)
self._create_text(
fig,
[0.87, 0.92, 1.5 * size_button, size_button],
"cmax = ",
self._change_cmax,
"{:.2f}".format(self.clim[1]),
)
self._create_text(
fig,
[0.87, 0.1, 1.5 * size_button, size_button],
"cmin = ",
self._change_cmin,
"{:.2f}".format(self.clim[0]),
)
self._create_button(
fig, [0.65, 0.945, 1.2 * size_button, 0.045], "reload", self.reloadim
)
self._create_button(
fig, [0.85, y, size_button, size_button], "auto", self.set_autoclim
)
cax = fig.add_axes([0.83, 0.2, 0.07, 0.7])
self.cbar = fig.colorbar(self.mappable, cax=cax)
fig.canvas.mpl_connect("key_press_event", self.onclick)
print("press alt+h for help")
plt.show()
def set_autoclim(self, event):
_print_debug("set_autoclim")
im = imread(self.path_files[self.ifile])
self.clim = [im.min(), 0.99 * im.max()]
self._update_clim()