def save_array(self, root, template):
# 1. iterate through planes in bulk
# 2. for each plane, save plane based on root, template
# 3. create path with url and add to gon
if not os.path.exists(root):
os.makedirs(root)
file_name = template.rv.format(self.experiment.name, self.series.name, self.channel.name, str_value(self.t, self.series.ts), '{}')
url = os.path.join(root, file_name)
if len(self.array.shape)==2:
imsave(url.format(str_value(self.z, self.series.zs)), self.array)
self.paths.create(composite=self.composite if self.composite is not None else self.gon.composite, channel=self.channel, template=template, url=url.format(str_value(self.z, self.series.zs)), file_name=file_name.format(str_value(self.z, self.series.zs)), t=self.t, z=self.z)
else:
for z in range(self.array.shape[2]):
plane = self.array[:,:,z].copy()
imsave(url.format(str_value(z+self.z, self.series.zs)), plane) # z level is offset by that of original gon.
self.paths.create(composite=self.composite, channel=self.channel, template=template, url=url.format(str_value(self.z, self.series.zs)), file_name=file_name.format(str_value(self.z, self.series.zs)), t=self.t, z=z+self.z)
# create gons
gon = self.gons.create(experiment=self.composite.experiment, series=self.composite.series, channel=self.channel, template=template)
gon.set_origin(self.r, self.c, z, self.t)
gon.set_extent(self.rs, self.cs, 1)
gon.array = plane.copy().squeeze()
gon.save_array(self.experiment.composite_path, template)
gon.save()
def mod_region_test(composite, mod_id, algorithm, **kwargs):
region_test_path = os.path.join(composite.experiment.video_path, "regions", composite.series.name)
if not os.path.exists(region_test_path):
os.makedirs(region_test_path)
for t in range(composite.series.ts):
zbf = composite.gons.get(t=t, channel__name="-zbf").load()
region_mask = composite.masks.get(t=t, channel__name__contains=kwargs["channel_unique_override"]).load()
mask_edges = mask_edge_image(region_mask)
zbf_mask_r = zbf.copy()
zbf_mask_g = zbf.copy()
zbf_mask_b = zbf.copy()
# edges
zbf_mask_r[mask_edges > 0] = 100
zbf_mask_g[mask_edges > 0] = 100
zbf_mask_b[mask_edges > 0] = 100
# region labels
# prepare drawing
blank_slate = np.zeros(zbf.shape)
blank_slate_img = Image.fromarray(blank_slate)
draw = ImageDraw.Draw(blank_slate_img)
for unique in [u for u in np.unique(region_mask) if u > 0]:
if (
composite.series.region_instances.filter(region_track_instance__t=t, mode_gray_value_id=unique).count()
> 0
):
region = composite.series.region_instances.get(
region_track_instance__t=t, mode_gray_value_id=unique
).region
# get coords (isolate mask, cut to black, use r/c)
isolated_mask = region_mask == unique
cut, (r0, c0, rs, cs) = cut_to_black(isolated_mask)
com_r, com_c = com(isolated_mask)
draw.text(
(com_c + 30, com_r + 30),
"{}".format(region.name),
font=ImageFont.load_default(),
fill="rgb(0,0,255)",
)
blank_slate = np.array(blank_slate_img)
zbf_mask_r[blank_slate > 0] = 0
zbf_mask_g[blank_slate > 0] = 0
zbf_mask_b[blank_slate > 0] = 255
whole = np.dstack([zbf_mask_r, zbf_mask_g, zbf_mask_b])
imsave(
join(
region_test_path,
"regions_{}_s{}_t{}.tiff".format(
composite.experiment.name, composite.series.name, str_value(t, composite.series.ts)
),
),
whole,
)
def mod_tile(composite, mod_id, algorithm, **kwargs):
tile_path = os.path.join(composite.experiment.video_path, "tile", composite.series.name)
if not os.path.exists(tile_path):
os.makedirs(tile_path)
for t in range(composite.series.ts):
zbf_gon = composite.gons.get(t=t, channel__name="-zbf")
zcomp_gon = composite.gons.get(t=t, channel__name="-zcomp")
zmean_gon = composite.gons.get(t=t, channel__name="-zmean")
mask_mask = composite.masks.get(t=t, channel__name__contains=kwargs["channel_unique_override"])
zbf = zbf_gon.load()
zcomp = zcomp_gon.load()
zmean = zmean_gon.load()
mask = mask_mask.load()
mask_outline = mask_edge_image(mask)
zbf_mask_r = zbf.copy()
zbf_mask_g = zbf.copy()
zbf_mask_b = zbf.copy()
zcomp_mask_r = zcomp.copy()
zcomp_mask_g = zcomp.copy()
zcomp_mask_b = zcomp.copy()
# drawing
# 1. draw outlines in red channel
zbf_mask_r[mask_outline > 0] = 255
zbf_mask_g[mask_outline > 0] = 0
zbf_mask_b[mask_outline > 0] = 0
zcomp_mask_r[mask_outline > 0] = 255
zcomp_mask_g[mask_outline > 0] = 0
zcomp_mask_b[mask_outline > 0] = 0
markers = composite.markers.filter(track_instance__t=t, track__cell__isnull=False)
for marker in markers:
if hasattr(marker.track_instance, "cell_instance"):
# 2. draw markers in blue channel
zbf_mask_r[marker.r - 2 : marker.r + 3, marker.c - 2 : marker.c + 3] = 0
zbf_mask_g[marker.r - 2 : marker.r + 3, marker.c - 2 : marker.c + 3] = 0
zbf_mask_b[marker.r - 2 : marker.r + 3, marker.c - 2 : marker.c + 3] = 255
zcomp_mask_r[marker.r - 2 : marker.r + 3, marker.c - 2 : marker.c + 3] = 0
zcomp_mask_g[marker.r - 2 : marker.r + 3, marker.c - 2 : marker.c + 3] = 0
zcomp_mask_b[marker.r - 2 : marker.r + 3, marker.c - 2 : marker.c + 3] = 255
# 3. draw text in green channel
blank_slate = np.zeros(zbf.shape)
blank_slate_img = Image.fromarray(blank_slate)
draw = ImageDraw.Draw(blank_slate_img)
draw.text(
(marker.c + 5, marker.r + 5),
"{}".format(marker.track.cell.pk),
font=ImageFont.load_default(),
fill="rgb(0,0,255)",
)
blank_slate = np.array(blank_slate_img)
zbf_mask_r[blank_slate > 0] = 0
zbf_mask_g[blank_slate > 0] = 255
zbf_mask_b[blank_slate > 0] = 0
zcomp_mask_r[blank_slate > 0] = 0
zcomp_mask_g[blank_slate > 0] = 255
zcomp_mask_b[blank_slate > 0] = 0
# regions
region_mask = composite.masks.get(t=t, channel__name__contains=composite.current_region_unique).load()
region_mask_edges = mask_edge_image(region_mask)
zbf_mask_r[region_mask_edges > 0] = 100
zbf_mask_g[region_mask_edges > 0] = 100
zbf_mask_b[region_mask_edges > 0] = 100
zcomp_mask_r[region_mask_edges > 0] = 100
zcomp_mask_g[region_mask_edges > 0] = 100
zcomp_mask_b[region_mask_edges > 0] = 100
# region labels
# prepare drawing
blank_slate = np.zeros(zbf.shape)
blank_slate_img = Image.fromarray(blank_slate)
draw = ImageDraw.Draw(blank_slate_img)
for unique in [u for u in np.unique(region_mask) if u > 0]:
if (
composite.series.region_instances.filter(region_track_instance__t=t, mode_gray_value_id=unique).count()
> 0
):
region = composite.series.region_instances.get(
region_track_instance__t=t, mode_gray_value_id=unique
).region
# get coords (isolate mask, cut to black, use r/c)
isolated_mask = region_mask == unique
cut, (r0, c0, rs, cs) = cut_to_black(isolated_mask)
draw.text(
(c0 + 30, r0 + 30), "{}".format(region.name), font=ImageFont.load_default(), fill="rgb(0,0,255)"
)
blank_slate = np.array(blank_slate_img)
zbf_mask_r[blank_slate > 0] = 0
zbf_mask_g[blank_slate > 0] = 0
zbf_mask_b[blank_slate > 0] = 255
zcomp_mask_r[blank_slate > 0] = 0
zcomp_mask_g[blank_slate > 0] = 0
zcomp_mask_b[blank_slate > 0] = 255
# tile zbf, zbf_mask, zcomp, zcomp_mask
top_half = np.concatenate((np.dstack([zbf, zbf, zbf]), np.dstack([zbf_mask_r, zbf_mask_g, zbf_mask_b])), axis=0)
bottom_half = np.concatenate(
(np.dstack([zmean, zmean, zmean]), np.dstack([zcomp_mask_r, zcomp_mask_g, zcomp_mask_b])), axis=0
)
whole = np.concatenate((top_half, bottom_half), axis=1)
imsave(
join(
tile_path,
"tile_{}_s{}_t{}.tiff".format(
composite.experiment.name, composite.series.name, str_value(t, composite.series.ts)
),
),
whole,
)
def save_array(self, root, template):
# 1. iterate through planes in bulk
# 2. for each plane, save plane based on root, template
# 3. create path with url and add to gon
if not os.path.exists(root):
os.makedirs(root)
self.file_name = template.rv.format(self.experiment.name, self.series.name, self.channel.name, str_value(self.t, self.series.ts), str_value(self.z, self.series.zs))
self.url = os.path.join(root, self.file_name)
imsave(self.url, self.array)
def create_region_tile(self, channel_unique_override, top_channel='-zbf', side_channel='-zunique', main_channel='-zunique'):
tile_path = join(self.experiment.video_path, 'regions', self.series.name, channel_unique_override)
if not exists(tile_path):
os.makedirs(tile_path)
for t in range(self.series.ts):
zbf_gon = self.gons.get(t=t, channel__name=top_channel)
zcomp_gon = self.gons.get(t=t, channel__name=side_channel)
zmean_gon = self.gons.get(t=t, channel__name=main_channel)
zbf = zbf_gon.load()
zbf = zbf if len(zbf.shape)==2 or (len(zbf.shape)==2 and zbf.shape[2]==2) else np.squeeze(zbf[:,:,0])
zcomp = zcomp_gon.load()
zcomp = zcomp if len(zcomp.shape)==2 or (len(zcomp.shape)==2 and zcomp.shape[2]==2) else np.squeeze(zcomp[:,:,0])
zmean = zmean_gon.load()
zmean = zmean if len(zmean.shape)==2 or (len(zmean.shape)==2 and zmean.shape[2]==2) else np.squeeze(zmean[:,:,0])
zbf_mask_r = zbf.copy()
zbf_mask_g = zbf.copy()
zbf_mask_b = zbf.copy()
zcomp_mask_r = zcomp.copy()
zcomp_mask_g = zcomp.copy()
zcomp_mask_b = zcomp.copy()
# draw regions
for region_instance in self.series.region_instances.filter(region_track_instance__t=t):
# load mask
mask = region_instance.masks.all()[0].load()
# get mask outline
mask_edge = edge_image(mask)
# draw outlines in blue channel
zbf_mask_r[mask_edge>0] = 0
zbf_mask_g[mask_edge>0] = 0
zbf_mask_b[mask_edge>0] = 255
zcomp_mask_r[mask_edge>0] = 0
zcomp_mask_g[mask_edge>0] = 0
zcomp_mask_b[mask_edge>0] = 255
# tile zbf, zbf_mask, zcomp, zcomp_mask
top_half = np.concatenate((np.dstack([zbf, zbf, zbf]), np.dstack([zbf_mask_r, zbf_mask_g, zbf_mask_b])), axis=0)
bottom_half = np.concatenate((np.dstack([zmean, zmean, zmean]), np.dstack([zcomp_mask_r, zcomp_mask_g, zcomp_mask_b])), axis=0)
whole = np.concatenate((top_half, bottom_half), axis=1)
imsave(join(tile_path, 'tile_{}_s{}_region-{}_t{}.tiff'.format(self.experiment.name, self.series.name, channel_unique_override, str_value(t, self.series.ts))), whole)
def create_tile(self, channel_unique_override, top_channel='-zbf', side_channel='-zunique', main_channel='-zedge', region_list=[]):
tile_path = join(self.experiment.video_path, 'tile', self.series.name, '{}-{}'.format(dt.datetime.now().strftime('%Y-%m-%d-%H-%M'), channel_unique_override))
if not exists(tile_path):
os.makedirs(tile_path)
for t in range(self.series.ts):
zbf_gon = self.gons.get(t=t, channel__name=top_channel)
zcomp_gon = self.gons.get(t=t, channel__name=side_channel)
zmean_gon = self.gons.get(t=t, channel__name=main_channel)
mask_mask = self.masks.get(t=t, channel__name__contains=channel_unique_override)
zbf = zbf_gon.load()
zbf = zbf if len(zbf.shape)==2 or (len(zbf.shape)==2 and zbf.shape[2]==2) else np.squeeze(zbf[:,:,0])
zcomp = zcomp_gon.load()
zcomp = zcomp if len(zcomp.shape)==2 or (len(zcomp.shape)==2 and zcomp.shape[2]==2) else np.squeeze(zcomp[:,:,0])
zmean = zmean_gon.load()
zmean = zmean if len(zmean.shape)==2 or (len(zmean.shape)==2 and zmean.shape[2]==2) else np.squeeze(zmean[:,:,0])
mask = mask_mask.load()
# remove cells in regions
if region_list:
for cell_mask in mask_mask.cell_masks.exclude(region__name__in=region_list):
mask[mask==cell_mask.gray_value_id] = 0 # delete masks from image if not in regions
mask_outline = mask_edge_image(mask)
zbf_mask_r = zbf.copy()
zbf_mask_g = zbf.copy()
zbf_mask_b = zbf.copy()
zcomp_mask_r = zcomp.copy()
zcomp_mask_g = zcomp.copy()
zcomp_mask_b = zcomp.copy()
# drawing
# 1. draw outlines in red channel
zbf_mask_r[mask_outline>0] = 255
zbf_mask_g[mask_outline>0] = 0
zbf_mask_b[mask_outline>0] = 0
zcomp_mask_r[mask_outline>0] = 255
zcomp_mask_g[mask_outline>0] = 0
zcomp_mask_b[mask_outline>0] = 0
# draw markers
markers = self.markers.filter(track_instance__t=t, track__cell__isnull=False)
for marker in markers:
if hasattr(marker.track_instance, 'cell_instance'):
if marker.track_instance.cell_instance.masks.filter(channel__name__contains=channel_unique_override):
if region_list==[] or (marker.track_instance.cell_instance.masks.get(channel__name__contains=channel_unique_override).region is not None and marker.track_instance.cell_instance.masks.get(channel__name__contains=channel_unique_override).region.name in region_list):
# 2. draw markers in blue channel
zbf_mask_r[marker.r-2:marker.r+3,marker.c-2:marker.c+3] = 0
zbf_mask_g[marker.r-2:marker.r+3,marker.c-2:marker.c+3] = 0
zbf_mask_b[marker.r-2:marker.r+3,marker.c-2:marker.c+3] = 255
zcomp_mask_r[marker.r-2:marker.r+3,marker.c-2:marker.c+3] = 0
zcomp_mask_g[marker.r-2:marker.r+3,marker.c-2:marker.c+3] = 0
zcomp_mask_b[marker.r-2:marker.r+3,marker.c-2:marker.c+3] = 255
# 3. draw text in green channel
blank_slate = np.zeros(zbf.shape)
blank_slate_img = Image.fromarray(blank_slate)
draw = ImageDraw.Draw(blank_slate_img)
draw.text((marker.c+5, marker.r+5), '{}'.format(marker.track.cell.pk), font=ImageFont.load_default(), fill='rgb(0,0,255)')
blank_slate = np.array(blank_slate_img)
zbf_mask_r[blank_slate>0] = 0
zbf_mask_g[blank_slate>0] = 255
zbf_mask_b[blank_slate>0] = 0
zcomp_mask_r[blank_slate>0] = 0
zcomp_mask_g[blank_slate>0] = 255
zcomp_mask_b[blank_slate>0] = 0
# draw regions
for region_instance in self.series.region_instances.filter(region_track_instance__t=t):
# load mask
mask = region_instance.masks.all()[0].load()
# get mask outline
mask_edge = edge_image(mask)
# draw outlines in blue channel
zbf_mask_r[mask_edge>0] = 0
zbf_mask_g[mask_edge>0] = 0
zbf_mask_b[mask_edge>0] = 255
zcomp_mask_r[mask_edge>0] = 0
zcomp_mask_g[mask_edge>0] = 0
zcomp_mask_b[mask_edge>0] = 255
# tile zbf, zbf_mask, zcomp, zcomp_mask
top_half = np.concatenate((np.dstack([zbf, zbf, zbf]), np.dstack([zbf_mask_r, zbf_mask_g, zbf_mask_b])), axis=0)
bottom_half = np.concatenate((np.dstack([zmean, zmean, zmean]), np.dstack([zcomp_mask_r, zcomp_mask_g, zcomp_mask_b])), axis=0)
whole = np.concatenate((top_half, bottom_half), axis=1)
imsave(join(tile_path, 'tile_{}_s{}_marker-{}_t{}.tiff'.format(self.experiment.name, self.series.name, channel_unique_override, str_value(t, self.series.ts))), whole)
