def test_resize_image(self, size):
w, h = 512, 512
data = numpy.zeros((h, w, 3), dtype=numpy.uint8)
data[256, 256] = [255, 0, 0]
img = Image.fromarray(data, 'RGB')
result = image_utils.resize_image(img, size[0], size[1])
assert result is not None
width, height = result.size
assert width == size[0]
assert height == size[1]
def createmovie_figure(conn, pixel_ids, t_indexes, z_start, z_end, width,
height, spacer, algorithm, stepping, scalebar,
overlay_colour, time_units, image_labels,
max_col_count):
"""
Makes the complete Movie figure: A canvas showing an image per row with
multiple columns showing frames from each image/movie. Labels obove each
frame to show the time-stamp of that frame in the specified units and
labels on the left name each image.
@param conn The OMERO session
@param pixel_ids A list of the Pixel IDs for the images in the
figure
@param t_indexes A list of tIndexes to display frames from
@param z_start Projection Z-start
@param z_end Projection Z-end
@param width Maximum width of panels
@param height Max height of panels
@param spacer Space between panels
@param algorithm Projection algorithm e.g. "MAXIMUMINTENSITY"
@param stepping Projecttion z-step
@param scalebar A number of microns for scale-bar
@param overlay_colour Color of the scale bar as tuple (255,255,255)
@param time_units A string such as "SECS"
@param image_labels A list of lists, corresponding to pixelIds, for
labelling each image with one or more strings.
"""
mode = "RGB"
white = (255, 255, 255)
# create a rendering engine
re = conn.createRenderingEngine()
query_service = conn.getQueryService()
row_panels = []
total_height = 0
total_width = 0
max_image_width = 0
physical_size_x = 0
for row, pixels_id in enumerate(pixel_ids):
log("Rendering row %d" % (row))
pixels = query_service.get("Pixels", pixels_id)
size_x = pixels.getSizeX().getValue()
size_y = pixels.getSizeY().getValue()
size_z = pixels.getSizeZ().getValue()
size_t = pixels.getSizeT().getValue()
if pixels.getPhysicalSizeX():
physical_x = pixels.getPhysicalSizeX().getValue()
units_x = pixels.getPhysicalSizeX().getSymbol()
else:
physical_x = 0
units_x = ""
if pixels.getPhysicalSizeY():
physical_y = pixels.getPhysicalSizeY().getValue()
units_y = pixels.getPhysicalSizeY().getSymbol()
else:
physical_y = 0
units_y = ""
log(" Pixel size: x: %s %s y: %s %s" %
(str(physical_x), units_x, str(physical_y), units_y))
if row == 0: # set values for primary image
physical_size_x = physical_x
physical_size_y = physical_y
else: # compare primary image with current one
if physical_size_x != physical_x or physical_size_y != physical_y:
log(" WARNING: Images have different pixel lengths. Scales"
" are not comparable.")
log(" Image dimensions (pixels): x: %d y: %d" % (size_x, size_y))
max_image_width = max(max_image_width, size_x)
# set up rendering engine with the pixels
re.lookupPixels(pixels_id)
if not re.lookupRenderingDef(pixels_id):
re.resetDefaults()
if not re.lookupRenderingDef(pixels_id):
raise "Failed to lookup Rendering Def"
re.load()
pro_start = z_start
pro_end = z_end
# make sure we're within Z range for projection.
if pro_end >= size_z:
pro_end = size_z - 1
if pro_start > size_z:
pro_start = 0
log(" WARNING: Current image has fewer Z-sections than the"
" primary image.")
# if we have an invalid z-range (start or end less than 0), show
# default Z only
if pro_start < 0 or pro_end < 0:
pro_start = re.getDefaultZ()
pro_end = pro_start
log(" Display Z-section: %d" % (pro_end + 1))
else:
log(" Projecting z range: %d - %d (max Z is %d)" %
(pro_start + 1, pro_end + 1, size_z))
# now get each channel in greyscale (or colour)
# a list of renderedImages (data as Strings) for the split-view row
rendered_images = []
for time in t_indexes:
if time >= size_t:
log(" WARNING: This image does not have Time frame: %d. "
"(max is %d)" % (time + 1, size_t))
else:
if pro_start != pro_end:
rendered_img = re.renderProjectedCompressed(
algorithm, time, stepping, pro_start, pro_end)
else:
plane_def = omero.romio.PlaneDef()
plane_def.z = pro_start
plane_def.t = time
rendered_img = re.renderCompressed(plane_def)
# create images and resize, add to list
image = Image.open(io.BytesIO(rendered_img))
resized_image = image_utils.resize_image(image, width, height)
rendered_images.append(resized_image)
# make a canvas for the row of splitview images...
# (will add time labels above each row)
col_count = min(max_col_count, len(rendered_images))
row_count = int(math.ceil(float(len(rendered_images)) / col_count))
font = image_utils.get_font(width / 12)
font_height = font.getsize("Textq")[1]
canvas_width = ((width + spacer) * col_count) + spacer
canvas_height = row_count * (spacer / 2 + font_height + spacer +
height)
size = (canvas_width, canvas_height)
# create a canvas of appropriate width, height
canvas = Image.new(mode, size, white)
# add text labels
query_service = conn.getQueryService()
text_x = spacer
text_y = spacer / 4
col_index = 0
time_labels = figUtil.getTimeLabels(query_service, pixels_id,
t_indexes, size_t, time_units)
for t, t_index in enumerate(t_indexes):
if t_index >= size_t:
continue
time = time_labels[t]
text_w = font.getsize(time)[0]
inset = (width - text_w) / 2
textdraw = ImageDraw.Draw(canvas)
textdraw.text((text_x + inset, text_y),
time,
font=font,
fill=(0, 0, 0))
text_x += width + spacer
col_index += 1
if col_index >= max_col_count:
col_index = 0
text_x = spacer
text_y += (spacer / 2 + font_height + spacer + height)
# add scale bar to last frame...
if scalebar:
scaled_image = rendered_images[-1]
x_indent = spacer
y_indent = x_indent
# if we've scaled to half size, zoom = 2
zoom = image_utils.get_zoom_factor(scaled_image.size, width,
height)
# and the scale bar will be half size
sbar = float(scalebar) / zoom
status, log_msg = figUtil.addScalebar(sbar, x_indent, y_indent,
scaled_image, pixels,
overlay_colour)
log(log_msg)
px = spacer
py = spacer + font_height
col_index = 0
# paste the images in
for i, img in enumerate(rendered_images):
image_utils.paste_image(img, canvas, px, py)
px = px + width + spacer
col_index += 1
if col_index >= max_col_count:
col_index = 0
px = spacer
py += (spacer / 2 + font_height + spacer + height)
# Add labels to the left of the panel
canvas = add_left_labels(canvas, image_labels, row, width, spacer)
# most should be same width anyway
total_width = max(total_width, canvas.size[0])
# add together the heights of each row
total_height = total_height + canvas.size[1]
row_panels.append(canvas)
# make a figure to combine all split-view rows
# each row has 1/2 spacer above and below the panels. Need extra 1/2
# spacer top and bottom
figure_size = (total_width, total_height + spacer)
figure_canvas = Image.new(mode, figure_size, white)
row_y = spacer / 2
for row in row_panels:
image_utils.paste_image(row, figure_canvas, 0, row_y)
row_y = row_y + row.size[1]
return figure_canvas
def get_split_view(conn,
pixel_ids,
z_start,
z_end,
split_indexes,
channel_names,
colour_channels,
merged_indexes,
merged_colours,
width=None,
height=None,
spacer=12,
algorithm=None,
stepping=1,
scalebar=None,
overlay_colour=(255, 255, 255)):
"""
This method makes a figure of a number of images, arranged in rows with
each row being the split-view of a single image. The channels are arranged
left to right, with the combined image added on the right.
The combined image is rendered according to current settings on the
server, but it's channels will be turned on/off according to
@merged_indexes.
No text labels are added to the image at this stage.
The figure is returned as a PIL 'Image'
@ conn session for server access
@ pixel_ids a list of the Ids for the pixels we want to display
@ z_start the start of Z-range for projection
@ z_end the end of Z-range for projection
@ split_indexes a list of the channel indexes to display. Same
channels for each image/row
@ channel_names the Map of index:names to go above the columns for
each split channel
@ colour_channels the colour to make each column/ channel
@ merged_indexes list or set of channels in the merged image
@ merged_colours index: colour dictionary of channels in the merged
image
@ width the size in pixels to show each panel
@ height the size in pixels to show each panel
@ spacer the gap between images and around the figure. Doubled
between rows.
"""
if algorithm is None: # omero::constants::projection::ProjectionType
algorithm = ProjectionType.MAXIMUMINTENSITY
timepoint = 0
mode = "RGB"
white = (255, 255, 255)
# create a rendering engine
re = conn.createRenderingEngine()
query_service = conn.getQueryService()
row_panels = []
total_height = 0
total_width = 0
max_image_width = 0
physical_size_x = 0
log("Split View Rendering Log...")
if z_start > -1 and z_end > -1:
al_string = str(algorithm).replace("INTENSITY",
" Intensity").capitalize()
log("All images projected using '%s' projection with step size: "
"%d start: %d end: %d" %
(al_string, stepping, z_start + 1, z_end + 1))
else:
log("Images show last-viewed Z-section")
for row, pixels_id in enumerate(pixel_ids):
log("Rendering row %d" % (row + 1))
pixels = query_service.get("Pixels", pixels_id)
size_x = pixels.getSizeX().getValue()
size_y = pixels.getSizeY().getValue()
size_z = pixels.getSizeZ().getValue()
size_c = pixels.getSizeC().getValue()
if pixels.getPhysicalSizeX():
physical_x = pixels.getPhysicalSizeX().getValue()
else:
physical_x = 0
if pixels.getPhysicalSizeY():
physical_y = pixels.getPhysicalSizeY().getValue()
else:
physical_y = 0
log(" Pixel size (um): x: %.3f y: %.3f" % (physical_x, physical_y))
if row == 0: # set values for primary image
physical_size_x = physical_x
physical_size_y = physical_y
else: # compare primary image with current one
if physical_size_x != physical_x or physical_size_y != physical_y:
log(" WARNING: Images have different pixel lengths."
" Scales are not comparable.")
log(" Image dimensions (pixels): x: %d y: %d" % (size_x, size_y))
max_image_width = max(max_image_width, size_x)
# set up rendering engine with the pixels
re.lookupPixels(pixels_id)
if not re.lookupRenderingDef(pixels_id):
re.resetDefaults()
if not re.lookupRenderingDef(pixels_id):
raise "Failed to lookup Rendering Def"
re.load()
pro_start = z_start
pro_end = z_end
# make sure we're within Z range for projection.
if pro_end >= size_z:
pro_end = size_z - 1
if pro_start > size_z:
pro_start = 0
log(" WARNING: Current image has fewer Z-sections than the"
" primary image.")
# if we have an invalid z-range (start or end less than 0), show
# default Z only
if pro_start < 0 or pro_end < 0:
pro_start = re.getDefaultZ()
pro_end = pro_start
log(" Display Z-section: %d" % (pro_end + 1))
else:
log(" Projecting z range: %d - %d (max Z is %d)" %
(pro_start + 1, pro_end + 1, size_z))
# turn on channels in merged_indexes
for i in range(size_c):
re.setActive(i, False) # Turn all off first
log("Turning on merged_indexes: %s ..." % merged_indexes)
for i in merged_indexes:
if i >= size_c:
channel_mismatch = True
else:
re.setActive(i, True)
if i in merged_colours:
re.setRGBA(i, *merged_colours[i])
# get the combined image, using the existing rendering settings
channels_string = ", ".join([channel_names[i] for i in merged_indexes])
log(" Rendering merged channels: %s" % channels_string)
if pro_start != pro_end:
overlay = re.renderProjectedCompressed(algorithm, timepoint,
stepping, pro_start,
pro_end)
else:
plane_def = omero.romio.PlaneDef()
plane_def.z = pro_start
plane_def.t = timepoint
overlay = re.renderCompressed(plane_def)
# now get each channel in greyscale (or colour)
# a list of renderedImages (data as Strings) for the split-view row
rendered_images = []
i = 0
channel_mismatch = False
# first, turn off all channels in pixels
for i in range(size_c):
re.setActive(i, False)
# for each channel in the splitview...
for index in split_indexes:
if index >= size_c:
# can't turn channel on - simply render black square!
channel_mismatch = True
rendered_images.append(None)
else:
re.setActive(index, True) # turn channel on
if colour_channels: # if split channels are coloured...
if index in merged_indexes:
# and this channel is in the combined image
if index in merged_colours:
rgba = tuple(merged_colours[index])
re.setRGBA(index, *rgba) # set coloured
else:
merged_colours[index] = re.getRGBA(index)
else:
# otherwise set white (max alpha)
re.setRGBA(index, 255, 255, 255, 255)
else:
# if not colour_channels - channels are white
re.setRGBA(index, 255, 255, 255, 255)
info = (index, re.getChannelWindowStart(index),
re.getChannelWindowEnd(index))
log(" Render channel: %s start: %d end: %d" % info)
if pro_start != pro_end:
rendered_img = re.renderProjectedCompressed(
algorithm, timepoint, stepping, pro_start, pro_end)
else:
plane_def = omero.romio.PlaneDef()
plane_def.z = pro_start
plane_def.t = timepoint
rendered_img = re.renderCompressed(plane_def)
rendered_images.append(rendered_img)
if index < size_c:
re.setActive(index, False) # turn the channel off again!
if channel_mismatch:
log(" WARNING channel mismatch: The current image has fewer"
" channels than the primary image.")
# make a canvas for the row of splitview images...
# extra image for combined image
image_count = len(rendered_images) + 1
canvas_width = ((width + spacer) * image_count) + spacer
canvas_height = spacer + height
size = (canvas_width, canvas_height)
# create a canvas of appropriate width, height
canvas = Image.new(mode, size, white)
px = spacer
py = spacer / 2
col = 0
# paste the images in
for img in rendered_images:
if img is None:
im = Image.new(mode, (size_x, size_y), (0, 0, 0))
else:
im = Image.open(io.BytesIO(img))
i = image_utils.resize_image(im, width, height)
image_utils.paste_image(i, canvas, px, py)
px = px + width + spacer
col = col + 1
# add combined image, after resizing and adding scale bar
i = Image.open(io.BytesIO(overlay))
scaled_image = image_utils.resize_image(i, width, height)
if scalebar:
x_indent = spacer
y_indent = x_indent
# if we've scaled to half size, zoom = 2
zoom = image_utils.get_zoom_factor(i.size, width, height)
# and the scale bar will be half size
sbar = float(scalebar) / zoom
status, log_msg = figUtil.addScalebar(sbar, x_indent, y_indent,
scaled_image, pixels,
overlay_colour)
log(log_msg)
image_utils.paste_image(scaled_image, canvas, px, py)
# most should be same width anyway
total_width = max(total_width, canvas_width)
# add together the heights of each row
total_height = total_height + canvas_height
row_panels.append(canvas)
# make a figure to combine all split-view rows
# each row has 1/2 spacer above and below the panels. Need extra 1/2
# spacer top and bottom
figure_size = (total_width, total_height + spacer)
figure_canvas = Image.new(mode, figure_size, white)
row_y = spacer / 2
for row in row_panels:
image_utils.paste_image(row, figure_canvas, 0, row_y)
row_y = row_y + row.size[1]
return figure_canvas
def get_split_view(conn, image_ids, pixel_ids, split_indexes, channel_names,
merged_names, colour_channels, merged_indexes,
merged_colours, width, height, image_labels, spacer,
algorithm, stepping, scalebar, overlay_colour, roi_zoom,
roi_label):
"""
This method makes a figure of a number of images, arranged in rows with
each row being the split-view of a single image. The channels are arranged
left to right, with the combined image added on the right.
The combined image is rendered according to current settings on the
server, but it's channels will be turned on/off according to
@mergedIndexes.
The figure is returned as a PIL 'Image'
@ session session for server access
@ pixel_ids a list of the Ids for the pixels we want to display
@ split_indexes a list of the channel indexes to display. Same
channels for each image/row
@ channel_names the Map of index:names for all channels
@ colour_channels the colour to make each column/ channel
@ merged_indexes list or set of channels in the merged image
@ merged_colours index: colour dictionary of channels in the merged
image
@ width the size in pixels to show each panel
@ height the size in pixels to show each panel
@ spacer the gap between images and around the figure. Doubled
between rows.
"""
roi_service = conn.getRoiService()
re = conn.createRenderingEngine()
query_service = conn.getQueryService() # only needed for movie
# establish dimensions and roiZoom for the primary image
# getTheseValues from the server
rect = get_rectangle(roi_service, image_ids[0], roi_label)
if rect is None:
raise Exception("No ROI found for the first image.")
roi_x, roi_y, roi_width, roi_height, y_min, y_max, t_min, t_max = rect
roi_outline = ((max(width, height)) / 200) + 1
if roi_zoom is None:
# get the pixels for priamry image.
pixels = query_service.get("Pixels", pixel_ids[0])
size_y = pixels.getSizeY().getValue()
roi_zoom = float(height) / float(roi_height)
log("ROI zoom set by primary image is %F X" % roi_zoom)
else:
log("ROI zoom: %F X" % roi_zoom)
text_gap = spacer / 3
fontsize = 12
if width > 500:
fontsize = 48
elif width > 400:
fontsize = 36
elif width > 300:
fontsize = 24
elif width > 200:
fontsize = 16
font = image_utils.get_font(fontsize)
text_height = font.getsize("Textq")[1]
max_count = 0
for row in image_labels:
max_count = max(max_count, len(row))
left_text_width = (text_height + text_gap) * max_count + spacer
max_split_panel_width = 0
total_canvas_height = 0
merged_images = []
roi_split_panes = []
top_spacers = [] # space for labels above each row
show_labels_above_every_row = False
invalid_images = [] # note any image row indexes that don't have ROIs.
for row, pixels_id in enumerate(pixel_ids):
log("Rendering row %d" % (row))
if show_labels_above_every_row:
show_top_labels = True
else:
show_top_labels = (row == 0) # only show top labels for first row
# need to get the roi dimensions from the server
image_id = image_ids[row]
roi = get_rectangle(roi_service, image_id, roi_label)
if roi is None:
log("No Rectangle ROI found for this image")
invalid_images.append(row)
continue
roi_x, roi_y, roi_width, roi_height, z_min, z_max, t_start, t_end = roi
pixels = query_service.get("Pixels", pixels_id)
size_x = pixels.getSizeX().getValue()
size_y = pixels.getSizeY().getValue()
z_start = z_min
z_end = z_max
# work out if any additional zoom is needed (if the full-sized image
# is different size from primary image)
full_size = (size_x, size_y)
image_zoom = image_utils.get_zoom_factor(full_size, width, height)
if image_zoom != 1.0:
log(" Scaling down the full-size image by a factor of %F" %
image_zoom)
log(" ROI location (top-left) x: %d y: %d and size width:"
" %d height: %d" % (roi_x, roi_y, roi_width, roi_height))
log(" ROI time: %d - %d zRange: %d - %d" %
(t_start + 1, t_end + 1, z_start + 1, z_end + 1))
# get the split pane and full merged image
roi_split_pane, full_merged_image, top_spacer = get_roi_split_view(
re, pixels, z_start, z_end, split_indexes, channel_names,
merged_names, colour_channels, merged_indexes, merged_colours,
roi_x, roi_y, roi_width, roi_height, roi_zoom, t_start, spacer,
algorithm, stepping, fontsize, show_top_labels)
# and now zoom the full-sized merged image, add scalebar
merged_image = image_utils.resize_image(full_merged_image, width,
height)
if scalebar:
x_indent = spacer
y_indent = x_indent
# and the scale bar will be half size
sbar = float(scalebar) / image_zoom
status, log_msg = figUtil.addScalebar(sbar, x_indent, y_indent,
merged_image, pixels,
overlay_colour)
log(log_msg)
# draw ROI onto mergedImage...
# recalculate roi if the image has been zoomed
x = roi_x / image_zoom
y = roi_y / image_zoom
roi_x2 = (roi_x + roi_width) / image_zoom
roi_y2 = (roi_y + roi_height) / image_zoom
draw_rectangle(merged_image, x, y, roi_x2, roi_y2, overlay_colour,
roi_outline)
# note the maxWidth of zoomed panels and total height for row
max_split_panel_width = max(max_split_panel_width,
roi_split_pane.size[0])
total_canvas_height += spacer + max(height + top_spacer,
roi_split_pane.size[1])
merged_images.append(merged_image)
roi_split_panes.append(roi_split_pane)
top_spacers.append(top_spacer)
# remove the labels for the invalid images (without ROIs)
invalid_images.reverse()
for row in invalid_images:
del image_labels[row]
# make a figure to combine all split-view rows
# each row has 1/2 spacer above and below the panels. Need extra 1/2
# spacer top and bottom
canvas_width = left_text_width + width + 2 * spacer + max_split_panel_width
figure_size = (canvas_width, total_canvas_height + spacer)
figure_canvas = Image.new("RGB", figure_size, (255, 255, 255))
row_y = spacer
for row, image in enumerate(merged_images):
label_canvas = figUtil.getVerticalLabels(image_labels[row], font,
text_gap)
v_offset = (image.size[1] - label_canvas.size[1]) / 2
image_utils.paste_image(label_canvas, figure_canvas, spacer / 2,
row_y + top_spacers[row] + v_offset)
image_utils.paste_image(image, figure_canvas, left_text_width,
row_y + top_spacers[row])
x = left_text_width + width + spacer
image_utils.paste_image(roi_split_panes[row], figure_canvas, x, row_y)
row_y = row_y + max(image.size[1] + top_spacers[row],
roi_split_panes[row].size[1]) + spacer
return figure_canvas