def setup_plot_ed(axis, gs_spec):
# set up a PlotEditor for the given axis
# subplot grid, with larger height preference for plot for
# each increased row to make sliders of approx equal size and
# align top borders of top images
rows_cols = gs_spec.get_rows_columns()
extra_rows = rows_cols[3] - rows_cols[2]
gs_plot = gridspec.GridSpecFromSubplotSpec(
2,
1,
subplot_spec=gs_spec,
height_ratios=(1, 10 + 14 * extra_rows),
hspace=0.1 / (extra_rows * 1.4 + 1))
# transform arrays to the given orthogonal direction
ax = fig.add_subplot(gs_plot[1, 0])
plot_support.hide_axes(ax)
plane = config.PLANE[axis]
arrs_3d, aspect, origin, scaling = \
plot_support.setup_images_for_plane(
plane,
(self.image5d[0], self.labels_img, self.borders_img))
img3d_transposed = arrs_3d[0]
labels_img_transposed = libmag.get_if_within(arrs_3d, 1)
borders_img_transposed = libmag.get_if_within(arrs_3d, 2)
# slider through image planes
ax_scroll = fig.add_subplot(gs_plot[0, 0])
plane_slider = Slider(ax_scroll,
plot_support.get_plane_axis(plane),
0,
len(img3d_transposed) - 1,
valfmt="%d",
valinit=0,
valstep=1)
# plot editor
max_size = max_sizes[axis] if max_sizes else None
plot_ed = plot_editor.PlotEditor(
ax,
img3d_transposed,
labels_img_transposed,
cmap_labels,
plane,
aspect,
origin,
self.update_coords,
self.refresh_images,
scaling,
plane_slider,
img3d_borders=borders_img_transposed,
cmap_borders=cmap_borders,
fn_show_label_3d=self.fn_show_label_3d,
interp_planes=self.interp_planes,
fn_update_intensity=self.update_color_picker,
max_size=max_size,
fn_status_bar=self.fn_status_bar)
return plot_ed
def update_btn(self):
"""Update text and color of button to interpolate planes.
"""
if any(self.bounds):
# show current values if any exist
self.btn.label.set_text("Fill {} {}\nID {}".format(
plot_support.get_plane_axis(self.plane), self.bounds,
self.label_id))
self.btn.label.set_fontsize("xx-small")
enable_btn(self.btn, all(self.bounds))
def handle_extracted_plane():
# get sub-plot and hide x/y axes
ax = axs
if libmag.is_seq(ax):
ax = axs[imgi]
plot_support.hide_axes(ax)
# multiple artists can be shown at each frame by collecting
# each group of artists in a list; overlay_images returns
# a nested list containing a list for each image, which in turn
# contains a list of artists for each channel
ax_imgs = plot_support.overlay_images(ax,
self.aspect,
self.origin,
imgs,
None,
cmaps_all,
ignore_invis=True,
check_single=True)
if (colorbar is not None and len(ax_imgs) > 0
and len(ax_imgs[0]) > 0 and imgi == 0):
# add colorbar with scientific notation if outside limits
cbar = ax.figure.colorbar(ax_imgs[0][0], ax=ax, **colorbar)
plot_support.set_scinot(cbar.ax, lbls=None, units=None)
plotted_imgs[imgi] = np.array(ax_imgs).flatten()
if libmag.is_seq(text_pos) and len(text_pos) > 1:
# write plane index in axes rather than data coordinates
text = ax.text(*text_pos[:2],
"{}-plane: {}".format(
plot_support.get_plane_axis(config.plane),
self.start_planei + imgi),
transform=ax.transAxes,
color="w")
plotted_imgs[imgi] = [*plotted_imgs[imgi], text]
if scale_bar:
plot_support.add_scale_bar(ax, 1 / self.rescale, config.plane)
def __str__(self):
return "{}: {} (ID: {})".format(
plot_support.get_plane_axis(self.plane), self.bounds,
self.label_id)
def stack_to_img(paths,
roi_offset,
roi_size,
series=None,
subimg_offset=None,
subimg_size=None,
animated=False,
suffix=None):
"""Build an image file from a stack of images in a directory or an
array, exporting as an animated GIF or movie for multiple planes or
extracting a single plane to a standard image file format.
Writes the file to the parent directory of path.
Args:
paths (List[str]): Image paths, which can each be either an image
directory or a base path to a single image, including
volumetric images.
roi_offset (Sequence[int]): Tuple of offset given in user order
``x,y,z``; defaults to None. Requires ``roi_size`` to not be None.
roi_size (Sequence[int]): Size of the region of interest in user order
``x,y,z``; defaults to None. Requires ``roi_offset`` to not be None.
series (int): Image series number; defaults to None.
subimg_offset (List[int]): Sub-image offset as (z,y,x) to load;
defaults to None.
subimg_size (List[int]): Sub-image size as (z,y,x) to load;
defaults to None.
animated (bool): True to export as an animated image; defaults to False.
suffix (str): String to append to output path before extension;
defaults to None to ignore.
"""
# set up figure layout for collages
size = config.plot_labels[config.PlotLabels.LAYOUT]
ncols, nrows = size if size else (1, 1)
num_paths = len(paths)
collage = num_paths > 1
figs = {}
for i in range(nrows):
for j in range(ncols):
n = i * ncols + j
if n >= num_paths: break
# load an image and set up its image stacker
path_sub = paths[n]
axs = []
# TODO: test directory of images
# TODO: consider not reloading first image
np_io.setup_images(path_sub, series, subimg_offset, subimg_size)
stacker = setup_stack(
config.image5d,
path_sub,
offset=roi_offset,
roi_size=roi_size,
slice_vals=config.slice_vals,
rescale=config.transform[config.Transforms.RESCALE],
labels_imgs=(config.labels_img, config.borders_img))
# add sub-plot title unless groups given as empty string
title = None
if config.groups:
title = libmag.get_if_within(config.groups, n)
elif num_paths > 1:
title = os.path.basename(path_sub)
if not stacker.images: continue
ax = None
for k in range(len(stacker.images[0])):
# create or retrieve fig; animation has only 1 fig
planei = 0 if animated else (stacker.img_slice.start +
k * stacker.img_slice.step)
fig_dict = figs.get(planei)
if not fig_dict:
# set up new fig
fig, gs = plot_support.setup_fig(
nrows, ncols,
config.plot_labels[config.PlotLabels.SIZE])
fig_dict = {"fig": fig, "gs": gs, "imgs": []}
figs[planei] = fig_dict
if ax is None:
# generate new axes for the gridspec position
ax = fig_dict["fig"].add_subplot(fig_dict["gs"][i, j])
if title:
ax.title.set_text(title)
axs.append(ax)
# export planes
plotted_imgs = stacker.build_stack(
axs, config.plot_labels[config.PlotLabels.SCALE_BAR],
size is None or ncols * nrows == 1)
if animated:
# store all plotted images in single fig
fig_dict = figs.get(0)
if fig_dict:
fig_dict["imgs"] = plotted_imgs
else:
# store one plotted image per fig; not used currently
for fig_dict, img in zip(figs.values(), plotted_imgs):
fig_dict["imgs"].append(img)
path_base = paths[0]
for planei, fig_dict in figs.items():
if animated:
# generate animated image (eg animated GIF or movie file)
animate_imgs(path_base, fig_dict["imgs"], config.delay,
config.savefig, suffix)
else:
# generate single figure with axis and plane index in filename
if collage:
# output filename as a collage of images
if not os.path.isdir(path_base):
path_base = os.path.dirname(path_base)
path_base = os.path.join(path_base, "collage")
# insert mod as suffix, then add any additional suffix;
# can use config.prefix_out for make_out_path prefix
mod = "_plane_{}{}".format(
plot_support.get_plane_axis(config.plane), planei)
out_path = libmag.make_out_path(path_base, suffix=mod)
if suffix:
out_path = libmag.insert_before_ext(out_path, suffix)
plot_support.save_fig(out_path,
config.savefig,
fig=fig_dict["fig"])
def setup_stack(
image5d: np.ndarray,
path: Optional[str] = None,
offset: Optional[Sequence[int]] = None,
roi_size: Optional[Sequence[int]] = None,
slice_vals: Optional[Sequence[int]] = None,
rescale: Optional[float] = None,
labels_imgs: Optional[Sequence[np.ndarray]] = None) -> StackPlaneIO:
"""Set up a stack of images for export to file.
Supports a stack of image files in a directory or a single volumetric image
and associated labels images.
Args:
image5d: Images as a 4/5D Numpy array (t,z,y,x[c]). Can be None if
``path`` is set.
path: Path to an image directory from which all files will be imported
in Python sorted order, taking precedence over ``imaged5d``;
defaults to None.
offset: Tuple of offset given in user order (x, y, z); defaults to
None. Requires ``roi_size`` to not be None.
roi_size: Size of the region of interest in user order (x, y, z);
defaults to None. Requires ``offset`` to not be None.
slice_vals: List from which to construct a slice object to
extract only a portion of the image. Defaults to None, which
will give the whole image. If ``offset`` and ``roi_size`` are
also given, ``slice_vals`` will only be used for its interval term.
rescale: Rescaling factor for each image, performed on a plane-by-plane
basis; defaults to None, in which case 1.0 will be used.
labels_imgs: Sequence of labels-based images as a Numpy z,y,x arrays,
typically including labels and borders images; defaults to None.
Returns:
Stack builder instance.
"""
print("Starting image stack setup")
# build "z" slice, which will be applied to the transposed image
interval = 1 # default to export each plane
if offset is not None and roi_size is not None:
# extract planes based on ROI settings
# transpose coordinates to given plane
_, arrs_1d = plot_support.transpose_images(
config.plane, arrs_1d=[offset[::-1], roi_size[::-1]])
offset = arrs_1d[0][::-1]
roi_size = arrs_1d[1][::-1]
# ROI offset and size take precedence over slice vals except
# for use of the interval term
if slice_vals is not None and len(slice_vals) > 2:
interval = slice_vals[2]
size = roi_size[2]
img_sl = slice(offset[2], offset[2] + size, interval)
if interval is not None and interval < 0:
# reverse start/stop order to iterate backward
img_sl = slice(img_sl.stop, img_sl.start, interval)
print("using ROI offset {}, size {}, {}".format(offset, size, img_sl))
elif slice_vals:
# build directly from slice vals, replacing start and step if None
sl = slice(*slice_vals)
sl = [sl.start, sl.stop, sl.step]
if sl[0] is None:
# default to start at beginning of stack
sl[0] = 0
if sl[2] is None:
# default to interval/step of 1
sl[2] = 1
img_sl = slice(*sl)
else:
# default to take the whole image stack
img_sl = slice(0, None, 1)
if rescale is None:
rescale = 1.0
aspect = None
origin = None
cmaps_labels = []
extracted_planes = []
start_planei = 0
if path and os.path.isdir(path):
# builds animations from all files in a directory
planes = sorted(glob.glob(os.path.join(path, "*")))[::interval]
_logger.info("Importing images from %s: %s", path, planes)
fnc = StackPlaneIO.import_img
extracted_planes.append(planes)
else:
# load images from path and extract ROI based on slice parameters,
# assuming 1st image is atlas, 2nd and beyond are labels-based
imgs = [image5d]
if labels_imgs is not None:
for img in labels_imgs:
if img is not None: imgs.append(img[None])
_setup_labels_cmaps(imgs, cmaps_labels)
main_shape = None # z,y,x shape of 1st image
for img in imgs:
sl = img_sl
img_shape = img.shape[1:4]
if main_shape:
if main_shape != img_shape:
# scale slice bounds to the first image's shape
scaling = np.divide(img_shape, main_shape)
axis = plot_support.get_plane_axis(config.plane, True)
sl = libmag.scale_slice(sl, scaling[axis], img_shape[axis])
else:
main_shape = img_shape
planes, aspect, origin = plot_support.extract_planes(
img, sl, plane=config.plane)
if offset is not None and roi_size is not None:
# get ROI using transposed coordinates on transposed planes;
# returns list
planes = planes[:, offset[1]:offset[1] + roi_size[1],
offset[0]:offset[0] + roi_size[0]]
extracted_planes.append(planes)
fnc = StackPlaneIO.process_plane
if img_sl.start:
start_planei = img_sl.start
# store in stack worker
stacker = StackPlaneIO()
StackPlaneIO.interp_order = config.transform[
config.Transforms.INTERPOLATION]
stacker.images = extracted_planes
stacker.fn_process = fnc
stacker.rescale = rescale
stacker.start_planei = start_planei
stacker.origin = origin
stacker.aspect = aspect
stacker.cmaps_labels = cmaps_labels
stacker.img_slice = img_sl
return stacker
def stack_to_img(paths,
roi_offset,
roi_size,
series=None,
subimg_offset=None,
subimg_size=None,
animated=False,
suffix=None):
"""Build an image file from a stack of images in a directory or an
array, exporting as an animated GIF or movie for multiple planes or
extracting a single plane to a standard image file format.
Writes the file to the parent directory of path.
Args:
paths (List[str]): Image paths, which can each be either an image
directory or a base path to a single image, including
volumetric images.
roi_offset (Sequence[int]): Tuple of offset given in user order
``x,y,z``; defaults to None. Requires ``roi_size`` to not be None.
roi_size (Sequence[int]): Size of the region of interest in user order
``x,y,z``; defaults to None. Requires ``roi_offset`` to not be None.
series (int): Image series number; defaults to None.
subimg_offset (List[int]): Sub-image offset as (z,y,x) to load;
defaults to None.
subimg_size (List[int]): Sub-image size as (z,y,x) to load;
defaults to None.
animated (bool): True to export as an animated image; defaults to False.
suffix (str): String to append to output path before extension;
defaults to None to ignore.
"""
size = config.plot_labels[config.PlotLabels.LAYOUT]
ncols, nrows = size if size else (1, 1)
fig, gs = plot_support.setup_fig(
nrows, ncols, config.plot_labels[config.PlotLabels.SIZE])
plotted_imgs = None
num_paths = len(paths)
for i in range(nrows):
for j in range(ncols):
n = i * ncols + j
if n >= num_paths: break
ax = fig.add_subplot(gs[i, j])
path_sub = paths[n]
# TODO: test directory of images
# TODO: avoid reloading first image
np_io.setup_images(path_sub, series, subimg_offset, subimg_size)
plotted_imgs = stack_to_ax_imgs(
ax,
config.image5d,
path_sub,
offset=roi_offset,
roi_size=roi_size,
slice_vals=config.slice_vals,
rescale=config.transform[config.Transforms.RESCALE],
labels_imgs=(config.labels_img, config.borders_img),
multiplane=animated,
fit=(size is None or ncols * nrows == 1))
path_base = paths[0]
if animated:
# generate animated image (eg animated GIF or movie file)
animate_imgs(path_base, plotted_imgs, config.delay, config.savefig,
suffix)
else:
# save image as single file
if roi_offset:
# get plane index from coordinate at the given axis in ROI offset
planei = roi_offset[::-1][plot_support.get_plane_axis(
config.plane, get_index=True)]
else:
# get plane index from slice start
planei = config.slice_vals[0]
if num_paths > 1:
# output filename as a collage of images
if not os.path.isdir(path_base):
path_base = os.path.dirname(path_base)
path_base = os.path.join(path_base, "collage")
mod = "_plane_{}{}".format(plot_support.get_plane_axis(config.plane),
planei)
if suffix: path_base = libmag.insert_before_ext(path_base, suffix)
plot_support.save_fig(path_base, config.savefig, mod)
def stack_to_ax_imgs(ax,
image5d,
path=None,
offset=None,
roi_size=None,
slice_vals=None,
rescale=None,
labels_imgs=None,
multiplane=False,
fit=False):
"""Export a stack of images in a directory or a single volumetric image
and associated labels images to :obj:`matplotlib.image.AxesImage`
objects for export.
Args:
ax (:obj:`plt.Axes`): Matplotlib axes on which to plot images.
image5d: Images as a 4/5D Numpy array (t,z,y,x[c]). Can be None if
``path`` is set.
path: Path to an image directory from which all files will be imported
in Python sorted order, taking precedence over ``imaged5d``;
defaults to None.
offset: Tuple of offset given in user order (x, y, z); defaults to
None. Requires ``roi_size`` to not be None.
roi_size: Size of the region of interest in user order (x, y, z);
defaults to None. Requires ``offset`` to not be None.
slice_vals: List from which to construct a slice object to
extract only a portion of the image. Defaults to None, which
will give the whole image. If ``offset`` and ``roi_size`` are
also given, ``slice_vals`` will only be used for its interval term.
rescale: Rescaling factor for each image, performed on a plane-by-plane
basis; defaults to None, in which case 1.0 will be used.
labels_imgs: Sequence of labels-based images as a Numpy z,y,x arrays,
typically including labels and borders images; defaults to None.
multiplane: True to extract the images as an animated GIF or movie
file; False to extract a single plane only. Defaults to False.
fit (bool): True to fit the figure frame to the resulting image.
Returns:
List[:obj:`matplotlib.image.AxesImage`]: List of image objects.
"""
print("Starting image stack export")
# build "z" slice, which will be applied to the transposed image;
# reduce image to 1 plane if in single mode
interval = 1
if offset is not None and roi_size is not None:
# transpose coordinates to given plane
_, arrs_1d = plot_support.transpose_images(
config.plane, arrs_1d=[offset[::-1], roi_size[::-1]])
offset = arrs_1d[0][::-1]
roi_size = arrs_1d[1][::-1]
# ROI offset and size take precedence over slice vals except
# for use of the interval term
interval = None
if slice_vals is not None and len(slice_vals) > 2:
interval = slice_vals[2]
size = roi_size[2] if multiplane else 1
img_sl = slice(offset[2], offset[2] + size, interval)
if interval is not None and interval < 0:
# reverse start/stop order to iterate backward
img_sl = slice(img_sl.stop, img_sl.start, interval)
print("using ROI offset {}, size {}, {}".format(offset, size, img_sl))
elif slice_vals is not None:
# build directly from slice vals unless not an animation
if multiplane:
img_sl = slice(*slice_vals)
else:
# single plane only for non-animation
img_sl = slice(slice_vals[0], slice_vals[0] + 1)
else:
# default to take the whole image stack
img_sl = slice(None, None)
if rescale is None:
rescale = 1.0
aspect = None
origin = None
cmaps_labels = []
extracted_planes = []
start_planei = 0
if path and os.path.isdir(path):
# builds animations from all files in a directory
planes = sorted(glob.glob(os.path.join(path, "*")))[::interval]
print(planes)
fnc = StackPlaneIO.import_img
extracted_planes.append(planes)
else:
# load images from path and extract ROI based on slice parameters,
# assuming 1st image is atlas, 2nd and beyond are labels-based
imgs = [image5d]
if labels_imgs is not None:
for img in labels_imgs:
if img is not None: imgs.append(img[None])
_setup_labels_cmaps(imgs, cmaps_labels)
main_shape = None # z,y,x shape of 1st image
for img in imgs:
sl = img_sl
img_shape = img.shape[1:4]
if main_shape:
if main_shape != img_shape:
# scale slice bounds to the first image's shape
scaling = np.divide(img_shape, main_shape)
axis = plot_support.get_plane_axis(config.plane, True)
sl = libmag.scale_slice(sl, scaling[axis], img_shape[axis])
else:
main_shape = img_shape
planes, aspect, origin = plot_support.extract_planes(
img, sl, plane=config.plane)
if offset is not None and roi_size is not None:
# get ROI using transposed coordinates on transposed planes;
# returns list
planes = planes[:, offset[1]:offset[1] + roi_size[1],
offset[0]:offset[0] + roi_size[0]]
extracted_planes.append(planes)
fnc = StackPlaneIO.process_plane
if img_sl.start:
start_planei = img_sl.start
# export planes
plotted_imgs = _build_stack(
ax,
extracted_planes,
fnc,
rescale,
aspect=aspect,
origin=origin,
cmaps_labels=cmaps_labels,
scale_bar=config.plot_labels[config.PlotLabels.SCALE_BAR],
start_planei=start_planei)
if fit and plotted_imgs:
# fit frame to first plane's first available image
ax_img = None
for ax_img in plotted_imgs[0]:
# images may be None if alpha set to 0
if ax_img is not None: break
if ax_img is not None:
plot_support.fit_frame_to_image(ax_img.figure,
ax_img.get_array().shape, aspect)
return plotted_imgs
def _build_stack(ax,
images,
process_fnc,
rescale=1,
aspect=None,
origin=None,
cmaps_labels=None,
scale_bar=True,
start_planei=0):
"""Builds a stack of Matploblit 2D images.
Uses multiprocessing to load or resize each image.
Args:
images: Sequence of images. For import, each "image" is a path to
and image file. For export, each "image" is a sequence of
planes, with the first sequence assumed to an atlas,
followed by labels-based images, each consisting of
corresponding planes.
process_fnc: Function to process each image through multiprocessing,
where the function should take an index and image and return the
index and processed plane.
rescale (float): Rescale factor; defaults to 1.
cmaps_labels: Sequence of colormaps for labels-based images;
defaults to None. Length should be equal to that of
``images`` - 1.
scale_bar: True to include scale bar; defaults to True.
start_planei (int): Index of start plane, used for labeling the
plane; defaults to 0. The plane is only annotated when
:attr:`config.plot_labels[config.PlotLabels.TEXT_POS]` is given
to specify the position of the text in ``x,y`` relative to the
axes.
Returns:
:List[List[:obj:`matplotlib.image.AxesImage`]]: Nested list of
axes image objects. The first list level contains planes, and
the second level are channels within each plane.
"""
# number of image types (eg atlas, labels) and corresponding planes
num_image_types = len(images)
if num_image_types < 1: return None
num_images = len(images[0])
if num_images < 1: return None
# Matplotlib figure for building the animation
plot_support.hide_axes(ax)
# import the images as Matplotlib artists via multiprocessing
plotted_imgs = [None] * num_images
img_shape = images[0][0].shape
target_size = np.multiply(img_shape, rescale).astype(int)
multichannel = images[0][0].ndim >= 3
if multichannel:
print("building stack for channel: {}".format(config.channel))
target_size = target_size[:-1]
StackPlaneIO.set_data(images)
pool = chunking.get_mp_pool()
pool_results = []
for i in range(num_images):
# add rotation argument if necessary
pool_results.append(
pool.apply_async(process_fnc, args=(i, target_size)))
# setup imshow parameters
colorbar = config.roi_profile["colorbar"]
cmaps_all = [config.cmaps, *cmaps_labels]
img_size = None
text_pos = config.plot_labels[config.PlotLabels.TEXT_POS]
for result in pool_results:
i, imgs = result.get()
if img_size is None: img_size = imgs[0].shape
# multiple artists can be shown at each frame by collecting
# each group of artists in a list; overlay_images returns
# a nested list containing a list for each image, which in turn
# contains a list of artists for each channel
ax_imgs = plot_support.overlay_images(ax,
aspect,
origin,
imgs,
None,
cmaps_all,
ignore_invis=True,
check_single=True)
if colorbar and len(ax_imgs) > 0 and len(ax_imgs[0]) > 0:
# add colorbar with scientific notation if outside limits
cbar = ax.figure.colorbar(ax_imgs[0][0], ax=ax, shrink=0.7)
plot_support.set_scinot(cbar.ax, lbls=None, units=None)
plotted_imgs[i] = np.array(ax_imgs).flatten()
if libmag.is_seq(text_pos) and len(text_pos) > 1:
# write plane index in axes rather than data coordinates
text = ax.text(*text_pos[:2],
"{}-plane: {}".format(
plot_support.get_plane_axis(config.plane),
start_planei + i),
transform=ax.transAxes,
color="w")
plotted_imgs[i] = [*plotted_imgs[i], text]
pool.close()
pool.join()
if scale_bar:
plot_support.add_scale_bar(ax, 1 / rescale, config.plane)
return plotted_imgs
