def extract_substack_no_rotation( job ):
""" Extracts a sub-stack as specified in the passed job without respecting
rotation requests. A list of pgmagick images is returned -- one for each
slice, starting on top.
"""
# The actual bounding boxes used for creating the images of each stack
# depend not only on the request, but also on the translation of the stack
# wrt. the project. Therefore, a dictionary with bounding box information for
# each stack is created.
s_to_bb = {}
for stack in job.stacks:
# Retrieve translation relative to current project
translation = ProjectStack.objects.get(
project_id=job.project_id, stack_id=stack.id).translation
x_min_t = job.x_min - translation.x
x_max_t = job.x_max - translation.x
y_min_t = job.y_min - translation.y
y_max_t = job.y_max - translation.y
z_min_t = job.z_min - translation.z
z_max_t = job.z_max - translation.z
# Calculate the slice numbers and pixel positions
# bound to the stack data.
px_x_min = to_x_index(x_min_t, job)
px_x_max = to_x_index(x_max_t, job)
px_y_min = to_y_index(y_min_t, job)
px_y_max = to_y_index(y_max_t, job)
px_z_min = to_z_index(z_min_t, job)
px_z_max = to_z_index(z_max_t, job)
# Because it might be that the cropping goes over the
# stack bounds, we need to calculate the unbounded height,
# with and an offset.
px_x_min_nobound = to_x_index(x_min_t, job, False)
px_x_max_nobound = to_x_index(x_max_t, job, False)
px_y_min_nobound = to_y_index(y_min_t, job, False)
px_y_max_nobound = to_y_index(y_max_t, job, False)
width = px_x_max_nobound - px_x_min_nobound
height = px_y_max_nobound - px_y_min_nobound
px_x_offset = abs(px_x_min_nobound) if px_x_min_nobound < 0 else 0
px_y_offset = abs(px_y_min_nobound) if px_y_min_nobound < 0 else 0
# Create a dictionary entry with a simple object
class BB: pass
bb = BB()
bb.px_x_min = px_x_min
bb.px_x_max = px_x_max
bb.px_y_min = px_y_min
bb.px_y_max = px_y_max
bb.px_z_min = px_z_min
bb.px_z_max = px_z_max
bb.px_x_offset = px_x_offset
bb.px_y_offset = px_y_offset
bb.width = width
bb.height = height
s_to_bb[stack.id] = bb
# Get number of wanted slices
px_z_min = to_z_index(job.z_min, job)
px_z_max = to_z_index(job.z_max, job)
n_slices = px_z_max + 1 - px_z_min
# The images are generated per slice, so most of the following
# calculations refer to 2d images.
# Each stack to export is treated as a separate channel. The order
# of the exported dimensions is XYCZ. This means all the channels of
# one slice are exported, then the next slice follows, etc.
cropped_stack = []
# Accumulator for estimated result size
estimated_total_size = 0
# Iterate over all slices
for nz in range(n_slices):
for stack in job.stacks:
bb = s_to_bb[stack.id]
# Shortcut for tile width and height
tile_width = stack.tile_width
tile_height = stack.tile_height
# Get indices for bounding tiles (0 indexed)
tile_x_min = int(bb.px_x_min / tile_width)
tile_x_max = int(bb.px_x_max / tile_width)
tile_y_min = int(bb.px_y_min / tile_height)
tile_y_max = int(bb.px_y_max / tile_height)
# Get the number of needed tiles for each direction
num_x_tiles = tile_x_max - tile_x_min + 1
num_y_tiles = tile_y_max - tile_y_min + 1
# Associate image parts with all tiles
image_parts = []
x_dst = bb.px_x_offset
for nx, x in enumerate( range(tile_x_min, tile_x_max + 1) ):
# The min x,y for the image part in the current tile are 0
# for all tiles except the first one.
cur_px_x_min = 0 if nx > 0 else bb.px_x_min - x * tile_width
# The max x,y for the image part of current tile are the tile
# size minus one except for the last one.
if nx < (num_x_tiles - 1):
cur_px_x_max = tile_width - 1
else:
cur_px_x_max = bb.px_x_max - x * tile_width
# Reset y destination component
y_dst = bb.px_y_offset
for ny, y in enumerate( range(tile_y_min, tile_y_max + 1) ):
cur_px_y_min = 0 if ny > 0 else bb.px_y_min - y * tile_height
if ny < (num_y_tiles - 1):
cur_px_y_max = tile_height - 1
else:
cur_px_y_max = bb.px_y_max - y * tile_height
# Create an image part definition
z = bb.px_z_min + nz
path = job.get_tile_path(stack, (x, y, z))
try:
part = ImagePart(path, cur_px_x_min, cur_px_x_max,
cur_px_y_min, cur_px_y_max, x_dst, y_dst)
image_parts.append( part )
except:
# ignore failed slices
pass
# Update y component of destination position
y_dst += cur_px_y_max - cur_px_y_min
# Update x component of destination position
x_dst += cur_px_x_max - cur_px_x_min
# Write out the image parts and make sure the maximum allowed file
# size isn't exceeded.
cropped_slice = None
for ip in image_parts:
# Get (correctly cropped) image
image = ip.get_image()
# Estimate total file size and abort if this exceeds the
# maximum allowed file size.
estimated_total_size = estimated_total_size + ip.estimated_size
if estimated_total_size > settings.GENERATED_FILES_MAXIMUM_SIZE:
raise ValueError("The estimated size of the requested image "
"region is larger than the maximum allowed "
"file size: %0.2f > %s Bytes" % \
(estimated_total_size,
settings.GENERATED_FILES_MAXIMUM_SIZE))
# It is unfortunately not possible to create proper composite
# images based on a canvas image newly created like this:
# cropped_slice = Image( Geometry(bb.width, bb.height), Color("black"))
# Therefore, this workaround is used.
if not cropped_slice:
cropped_slice = Image(image)
cropped_slice.backgroundColor("black")
cropped_slice.erase()
# The '!' makes sure the aspect ration is ignored
cropped_slice.scale('%sx%s!' % (bb.width, bb.height))
# Draw the image onto result image
cropped_slice.composite( image, ip.x_dst, ip.y_dst, co.OverCompositeOp )
# Delete tile image - it's not needed anymore
del image
if cropped_slice:
# Optionally, use only a single channel
if job.single_channel:
cropped_slice.channel( ChannelType.RedChannel )
# Add the image to the cropped stack
cropped_stack.append( cropped_slice )
return cropped_stack
def extract_substack_no_rotation(job) -> List:
""" Extracts a sub-stack as specified in the passed job without respecting
rotation requests. A list of pgmagick images is returned -- one for each
slice, starting on top.
"""
# The actual bounding boxes used for creating the images of each stack
# depend not only on the request, but also on the translation of the stack
# wrt. the project. Therefore, a dictionary with bounding box information for
# each stack is created.
s_to_bb = {}
for stack_mirror in job.stack_mirrors:
stack = stack_mirror.stack
# Retrieve translation relative to current project
translation = ProjectStack.objects.get(project_id=job.project_id,
stack_id=stack.id).translation
x_min_t = job.x_min - translation.x
x_max_t = job.x_max - translation.x
y_min_t = job.y_min - translation.y
y_max_t = job.y_max - translation.y
z_min_t = job.z_min - translation.z
z_max_t = job.z_max - translation.z
# Calculate the slice numbers and pixel positions
# bound to the stack data.
px_x_min = to_x_index(x_min_t, stack, job.zoom_level)
px_x_max = to_x_index(x_max_t, stack, job.zoom_level)
px_y_min = to_y_index(y_min_t, stack, job.zoom_level)
px_y_max = to_y_index(y_max_t, stack, job.zoom_level)
px_z_min = to_z_index(z_min_t, stack, job.zoom_level)
px_z_max = to_z_index(z_max_t, stack, job.zoom_level)
# Because it might be that the cropping goes over the
# stack bounds, we need to calculate the unbounded height,
# with and an offset.
px_x_min_nobound = to_x_index(x_min_t, stack, job.zoom_level, False)
px_x_max_nobound = to_x_index(x_max_t, stack, job.zoom_level, False)
px_y_min_nobound = to_y_index(y_min_t, stack, job.zoom_level, False)
px_y_max_nobound = to_y_index(y_max_t, stack, job.zoom_level, False)
width = px_x_max_nobound - px_x_min_nobound
height = px_y_max_nobound - px_y_min_nobound
px_x_offset = abs(px_x_min_nobound) if px_x_min_nobound < 0 else 0
px_y_offset = abs(px_y_min_nobound) if px_y_min_nobound < 0 else 0
# Create a dictionary entry with a simple object
bb = BB()
bb.px_x_min = px_x_min
bb.px_x_max = px_x_max
bb.px_y_min = px_y_min
bb.px_y_max = px_y_max
bb.px_z_min = px_z_min
bb.px_z_max = px_z_max
bb.px_x_offset = px_x_offset
bb.px_y_offset = px_y_offset
bb.width = width
bb.height = height
s_to_bb[stack.id] = bb
# Get number of wanted slices
px_z_min = to_z_index(job.z_min, job.ref_stack, job.zoom_level)
px_z_max = to_z_index(job.z_max, job.ref_stack, job.zoom_level)
n_slices = px_z_max + 1 - px_z_min
# The images are generated per slice, so most of the following
# calculations refer to 2d images.
# Each stack to export is treated as a separate channel. The order
# of the exported dimensions is XYCZ. This means all the channels of
# one slice are exported, then the next slice follows, etc.
cropped_stack = []
# Accumulator for estimated result size
estimated_total_size = 0
# Iterate over all slices
for nz in range(n_slices):
for mirror in job.stack_mirrors:
stack = mirror.stack
bb = s_to_bb[stack.id]
# Shortcut for tile width and height
tile_width = mirror.tile_width
tile_height = mirror.tile_height
# Get indices for bounding tiles (0 indexed)
tile_x_min = int(bb.px_x_min / tile_width)
tile_x_max = int(bb.px_x_max / tile_width)
tile_y_min = int(bb.px_y_min / tile_height)
tile_y_max = int(bb.px_y_max / tile_height)
# Get the number of needed tiles for each direction
num_x_tiles = tile_x_max - tile_x_min + 1
num_y_tiles = tile_y_max - tile_y_min + 1
# Associate image parts with all tiles
image_parts = []
x_dst = bb.px_x_offset
for nx, x in enumerate(range(tile_x_min, tile_x_max + 1)):
# The min x,y for the image part in the current tile are 0
# for all tiles except the first one.
cur_px_x_min = 0 if nx > 0 else bb.px_x_min - x * tile_width
# The max x,y for the image part of current tile are the tile
# size minus one except for the last one.
if nx < (num_x_tiles - 1):
cur_px_x_max = tile_width - 1
else:
cur_px_x_max = bb.px_x_max - x * tile_width
# Reset y destination component
y_dst = bb.px_y_offset
for ny, y in enumerate(range(tile_y_min, tile_y_max + 1)):
cur_px_y_min = 0 if ny > 0 else bb.px_y_min - y * tile_height
if ny < (num_y_tiles - 1):
cur_px_y_max = tile_height - 1
else:
cur_px_y_max = bb.px_y_max - y * tile_height
# Create an image part definition
z = bb.px_z_min + nz
path = job.get_tile_path(stack, mirror, (x, y, z))
try:
part = ImagePart(path, cur_px_x_min, cur_px_x_max,
cur_px_y_min, cur_px_y_max, x_dst,
y_dst)
image_parts.append(part)
except:
# ignore failed slices
pass
# Update y component of destination position
y_dst += cur_px_y_max - cur_px_y_min
# Update x component of destination position
x_dst += cur_px_x_max - cur_px_x_min
# Write out the image parts and make sure the maximum allowed file
# size isn't exceeded.
cropped_slice = Image(Geometry(bb.width, bb.height),
ColorRGB(0, 0, 0))
for ip in image_parts:
# Get (correctly cropped) image
image = ip.get_image()
# Estimate total file size and abort if this exceeds the
# maximum allowed file size.
estimated_total_size = estimated_total_size + ip.estimated_size
if estimated_total_size > settings.GENERATED_FILES_MAXIMUM_SIZE:
raise ValueError("The estimated size of the requested image "
"region is larger than the maximum allowed "
"file size: %0.2f > %s Bytes" % \
(estimated_total_size,
settings.GENERATED_FILES_MAXIMUM_SIZE))
# Draw the image onto result image
cropped_slice.composite(image, ip.x_dst, ip.y_dst,
co.OverCompositeOp)
# Delete tile image - it's not needed anymore
del image
if cropped_slice:
# Optionally, use only a single channel
if job.single_channel:
cropped_slice.channel(ChannelType.RedChannel)
# Add the image to the cropped stack
cropped_stack.append(cropped_slice)
return cropped_stack
def extract_substack_no_rotation(job):
""" Extracts a sub-stack as specified in the passed job without respecting
rotation requests. A list of pgmagick images is returned -- one for each
slice, starting on top.
"""
# The actual bounding boxes used for creating the images of each stack
# depend not only on the request, but also on the translation of the stack
# wrt. the project. Therefore, a dictionary with bounding box information for
# each stack is created.
s_to_bb = {}
for stack in job.stacks:
# Retrieve translation relative to current project
translation = ProjectStack.objects.get(project_id=job.project_id,
stack_id=stack.id).translation
x_min_t = job.x_min - translation.x
x_max_t = job.x_max - translation.x
y_min_t = job.y_min - translation.y
y_max_t = job.y_max - translation.y
z_min_t = job.z_min - translation.z
z_max_t = job.z_max - translation.z
# Calculate the slice numbers and pixel positions
# bound to the stack data.
px_x_min = to_x_index(x_min_t, job)
px_x_max = to_x_index(x_max_t, job)
px_y_min = to_y_index(y_min_t, job)
px_y_max = to_y_index(y_max_t, job)
px_z_min = to_z_index(z_min_t, job)
px_z_max = to_z_index(z_max_t, job)
# Because it might be that the cropping goes over the
# stack bounds, we need to calculate the unbounded height,
# with and an offset.
px_x_min_nobound = to_x_index(x_min_t, job, False)
px_x_max_nobound = to_x_index(x_max_t, job, False)
px_y_min_nobound = to_y_index(y_min_t, job, False)
px_y_max_nobound = to_y_index(y_max_t, job, False)
width = px_x_max_nobound - px_x_min_nobound
height = px_y_max_nobound - px_y_min_nobound
px_x_offset = abs(px_x_min_nobound) if px_x_min_nobound < 0 else 0
px_y_offset = abs(px_y_min_nobound) if px_y_min_nobound < 0 else 0
# Create a dictionary entry with a simple object
class BB:
pass
bb = BB()
bb.px_x_min = px_x_min
bb.px_x_max = px_x_max
bb.px_y_min = px_y_min
bb.px_y_max = px_y_max
bb.px_z_min = px_z_min
bb.px_z_max = px_z_max
bb.px_x_offset = px_x_offset
bb.px_y_offset = px_y_offset
bb.width = width
bb.height = height
s_to_bb[stack.id] = bb
# Get number of wanted slices
px_z_min = to_z_index(job.z_min, job)
px_z_max = to_z_index(job.z_max, job)
n_slices = px_z_max + 1 - px_z_min
# The images are generated per slice, so most of the following
# calculations refer to 2d images.
# Each stack to export is treated as a separate channel. The order
# of the exported dimensions is XYCZ. This means all the channels of
# one slice are exported, then the next slice follows, etc.
cropped_stack = []
# Iterate over all slices
for nz in range(n_slices):
for stack in job.stacks:
bb = s_to_bb[stack.id]
# Shortcut for tile width and height
tile_width = stack.tile_width
tile_height = stack.tile_height
# Get indices for bounding tiles (0 indexed)
tile_x_min = int(bb.px_x_min / tile_width)
tile_x_max = int(bb.px_x_max / tile_width)
tile_y_min = int(bb.px_y_min / tile_height)
tile_y_max = int(bb.px_y_max / tile_height)
# Get the number of needed tiles for each direction
num_x_tiles = tile_x_max - tile_x_min + 1
num_y_tiles = tile_y_max - tile_y_min + 1
# Associate image parts with all tiles
image_parts = []
x_dst = bb.px_x_offset
for nx, x in enumerate(range(tile_x_min, tile_x_max + 1)):
# The min x,y for the image part in the current tile are 0
# for all tiles except the first one.
cur_px_x_min = 0 if nx > 0 else bb.px_x_min - x * tile_width
# The max x,y for the image part of current tile are the tile
# size minus one except for the last one.
if nx < (num_x_tiles - 1):
cur_px_x_max = tile_width - 1
else:
cur_px_x_max = bb.px_x_max - x * tile_width
# Reset y destination component
y_dst = bb.px_y_offset
for ny, y in enumerate(range(tile_y_min, tile_y_max + 1)):
cur_px_y_min = 0 if ny > 0 else bb.px_y_min - y * tile_height
if ny < (num_y_tiles - 1):
cur_px_y_max = tile_height - 1
else:
cur_px_y_max = bb.px_y_max - y * tile_height
# Create an image part definition
z = bb.px_z_min + nz
path = job.get_tile_path(stack, (x, y, z))
try:
part = ImagePart(path, cur_px_x_min, cur_px_x_max,
cur_px_y_min, cur_px_y_max, x_dst,
y_dst)
image_parts.append(part)
except:
# ignore failed slices
pass
# Update y component of destination position
y_dst += cur_px_y_max - cur_px_y_min
# Update x component of destination position
x_dst += cur_px_x_max - cur_px_x_min
# write out the image parts
cropped_slice = None
for ip in image_parts:
# Get (correctly cropped) image
image = ip.get_image()
# It is unfortunately not possible to create proper composite
# images based on a canvas image newly created like this:
# cropped_slice = Image( Geometry(bb.width, bb.height), Color("black"))
# Therefore, this workaround is used.
if not cropped_slice:
cropped_slice = Image(image)
cropped_slice.backgroundColor("black")
cropped_slice.erase()
# The '!' makes sure the aspect ration is ignored
cropped_slice.scale('%sx%s!' % (bb.width, bb.height))
# Draw the image onto result image
cropped_slice.composite(image, ip.x_dst, ip.y_dst,
co.OverCompositeOp)
# Delete tile image - it's not needed anymore
del image
# Optionally, use only a single channel
if job.single_channel:
cropped_slice.channel(ChannelType.RedChannel)
# Add the image to the cropped stack
cropped_stack.append(cropped_slice)
return cropped_stack
def extract_substack_no_rotation( job ):
""" Extracts a sub-stack as specified in the passed job without respecting
rotation requests. A list of pgmagick images is returned -- one for each
slice, starting on top.
"""
# Calculate the slice numbers and pixel positions
# bounded to the stack data.
px_x_min = to_x_index(job.x_min, job)
px_x_max = to_x_index(job.x_max, job)
px_y_min = to_y_index(job.y_min, job)
px_y_max = to_y_index(job.y_max, job)
px_z_min = to_z_index(job.z_min, job)
px_z_max = to_z_index(job.z_max, job)
# Because it might be that the cropping goes over the
# stack bounds, we need to calculate the unbounded height,
# with and an offset.
px_x_min_nobound = to_x_index(job.x_min, job, False)
px_x_max_nobound = to_x_index(job.x_max, job, False)
px_y_min_nobound = to_y_index(job.y_min, job, False)
px_y_max_nobound = to_y_index(job.y_max, job, False)
width = px_x_max_nobound - px_x_min_nobound
height = px_y_max_nobound - px_y_min_nobound
px_x_offset = abs(px_x_min_nobound) if px_x_min_nobound < 0 else 0
px_y_offset = abs(px_y_min_nobound) if px_y_min_nobound < 0 else 0
# The images are generated per slice, so most of the following
# calculations refer to 2d images.
# Each stack to export is treated as a seperate channel. The order
# of the exported dimensions is XYCZ. This means all the channels of
# one slice are exported, then the next slice follows, etc.
cropped_stack = []
# Iterate over all slices
for z in range( px_z_min, px_z_max + 1):
for stack in job.stacks:
tile_width = stack.tile_width
tile_height = stack.tile_height
# Get indices for bounding tiles (0 indexed)
tile_x_min = int(px_x_min / tile_width)
tile_x_max = int(px_x_max / tile_width)
tile_y_min = int(px_y_min / tile_height)
tile_y_max = int(px_y_max / tile_height)
# Get the number of needed tiles for each direction
num_x_tiles = tile_x_max - tile_x_min + 1
num_y_tiles = tile_y_max - tile_y_min + 1
# Associate image parts with all tiles
image_parts = []
x_dst = px_x_offset
for nx, x in enumerate( range(tile_x_min, tile_x_max + 1) ):
# The min x,y for the image part in the current tile are 0
# for all tiles except the first one.
cur_px_x_min = 0 if nx > 0 else px_x_min - x * tile_width
# The max x,y for the image part of current tile are the tile
# size minus one except for the last one.
if nx < (num_x_tiles - 1):
cur_px_x_max = tile_width - 1
else:
cur_px_x_max = px_x_max - x * tile_width
# Reset y destination component
y_dst = px_y_offset
for ny, y in enumerate( range(tile_y_min, tile_y_max + 1) ):
cur_px_y_min = 0 if ny > 0 else px_y_min - y * tile_height
if ny < (num_y_tiles - 1):
cur_px_y_max = tile_height - 1
else:
cur_px_y_max = px_y_max - y * tile_height
# Create an image part definition
path = get_tile_path(job, stack, [x, y, z])
try:
part = ImagePart(path, cur_px_x_min, cur_px_x_max, cur_px_y_min, cur_px_y_max, x_dst, y_dst)
image_parts.append( part )
except:
# ignore failed slices
pass
# Update y component of destination postition
y_dst += cur_px_y_max - cur_px_y_min
# Update x component of destination postition
x_dst += cur_px_x_max - cur_px_x_min
# Create a result image slice, painted black
cropped_slice = Image( Geometry( width, height ), Color("black") )
# write out the image parts
for ip in image_parts:
# Get (correcly cropped) image
image = ip.get_image()
# Draw the image onto result image
cropped_slice.composite( image, ip.x_dst, ip.y_dst, co.OverCompositeOp )
# Delete tile image - it's not needed anymore
del image
# Optionally, use only a single channel
if job.single_channel:
cropped_slice.channel( ChannelType.RedChannel )
# Add the imag to the cropped stack
cropped_stack.append( cropped_slice )
return cropped_stack
