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Figure_To_Pdf.py
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Figure_To_Pdf.py
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#
# Copyright (c) 2014-2015 University of Dundee.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import logging
import json
import unicodedata
import numpy
from datetime import datetime
import os
from os import path
import zipfile
from math import atan2, atan, sin, cos, sqrt, radians
from omero.model import ImageAnnotationLinkI, ImageI
import omero.scripts as scripts
from omero.gateway import BlitzGateway
from omero.rtypes import rstring, robject
from cStringIO import StringIO
try:
from PIL import Image, ImageDraw, ImageFont
except ImportError:
import Image
import ImageDraw
logger = logging.getLogger('figure_to_pdf')
try:
import markdown
markdown_imported = True
except ImportError:
markdown_imported = False
logger.error("Markdown not installed. See"
" https://pypi.python.org/pypi/Markdown")
try:
from reportlab.pdfgen import canvas
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.platypus import Paragraph
from reportlab.lib.enums import TA_LEFT, TA_CENTER, TA_RIGHT
reportlab_installed = True
except ImportError:
reportlab_installed = False
logger.error("Reportlab not installed.")
DEFAULT_OFFSET = 0
ORIGINAL_DIR = "1_originals"
RESAMPLED_DIR = "2_pre_resampled"
FINAL_DIR = "3_final"
README_TXT = """These folders contain images used in the creation
of the figure. Each folder contains one image per figure panel,
with images numbered according to the order they were added to
the figure. The numbered folders represent the sequence of
processing steps:
- 1_originals: This contains the full-sized and un-cropped images that are
rendered by OMERO according to your chosen rendering settings.
- 2_pre_resampled: This folder will only contain those images that are
resampled in order to match the export figure resolution. This will be
all panels for export of TIFF figures. For export of PDF Figures,
only panels that have a 'dpi' set, which is higher than their
existing resolution will be resampled.
- 3_final: These are the image panels that are inserted into the
final figure, saved following any cropping, rotation and resampling steps.
"""
def scale_to_export_dpi(pixels):
"""
Original figure coordinates assume 72 dpi figure, but we want to
export at 300 dpi, so everything needs scaling accordingly
"""
return pixels * 300/72
def compress(target, base):
"""
Creates a ZIP recursively from a given base directory.
@param target: Name of the zip file we want to write E.g.
"folder.zip"
@param base: Name of folder that we want to zip up E.g. "folder"
"""
zip_file = zipfile.ZipFile(target, 'w')
try:
for root, dirs, files in os.walk(base):
archive_root = os.path.relpath(root, base)
for f in files:
fullpath = os.path.join(root, f)
archive_name = os.path.join(archive_root, f)
zip_file.write(fullpath, archive_name)
finally:
zip_file.close()
class ShapeToPdfExport(object):
def __init__(self, canvas, panel, page, crop, page_height):
self.canvas = canvas
self.panel = panel
self.page = page
# The crop region on the original image coordinates...
self.crop = crop
self.page_height = page_height
# Get a mapping from original coordinates to the actual size of panel
self.scale = float(panel['width']) / crop['width']
if "shapes" in panel:
for shape in panel["shapes"]:
if shape['type'] == "Arrow":
self.draw_arrow(shape)
elif shape['type'] == "Line":
self.draw_line(shape)
elif shape['type'] == "Rectangle":
self.draw_rectangle(shape)
elif shape['type'] == "Ellipse":
self.draw_ellipse(shape)
elif shape['type'] == "Polygon":
self.draw_polygon(shape)
elif shape['type'] == "Polyline":
self.draw_polyline(shape)
@staticmethod
def get_rgb(color):
# Convert from E.g. '#ff0000' to (255, 0, 0)
red = int(color[1:3], 16)
green = int(color[3:5], 16)
blue = int(color[5:7], 16)
return (red, green, blue)
def panel_to_page_coords(self, shape_x, shape_y):
"""
Convert coordinate from the image onto the PDF page.
Handles zoom, offset & rotation of panel, rotating the
x, y point around the centre of the cropped region
and scaling appropriately.
Also includes 'inPanel' key - True if point within
the cropped panel region
"""
rotation = self.panel['rotation']
if rotation != 0:
# img coords: centre of rotation
cx = self.crop['x'] + (self.crop['width']/2)
cy = self.crop['y'] + (self.crop['height']/2)
dx = cx - shape_x
dy = cy - shape_y
# distance of point from centre of rotation
h = sqrt(dx * dx + dy * dy)
# and the angle
angle1 = atan2(dx, dy)
# Add the rotation to the angle and calculate new
# opposite and adjacent lengths from centre of rotation
angle2 = angle1 - radians(rotation)
newo = sin(angle2) * h
newa = cos(angle2) * h
# to give correct x and y within cropped panel
shape_x = cx - newo
shape_y = cy - newa
# convert to coords within crop region
shape_x = shape_x - self.crop['x']
shape_y = shape_y - self.crop['y']
# check if points are within panel
in_panel = True
if shape_x < 0 or shape_x > self.crop['width']:
in_panel = False
if shape_y < 0 or shape_y > self.crop['height']:
in_panel = False
# Handle page offsets
x = self.panel['x'] - self.page['x']
y = self.panel['y'] - self.page['y']
# scale and position on page within panel
shape_x = (shape_x * self.scale) + x
shape_y = (shape_y * self.scale) + y
return {'x': shape_x, 'y': shape_y, 'inPanel': in_panel}
def draw_rectangle(self, shape):
top_left = self.panel_to_page_coords(shape['x'], shape['y'])
# Don't draw if all corners are outside the panel
top_right = self.panel_to_page_coords(shape['x'] + shape['width'],
shape['y'])
bottom_left = self.panel_to_page_coords(shape['x'],
shape['y'] + shape['height'])
bottom_right = self.panel_to_page_coords(shape['x'] + shape['width'],
shape['y'] + shape['height'])
if (top_left['inPanel'] is False) and (
top_right['inPanel'] is False) and (
bottom_left['inPanel'] is False) and (
bottom_right['inPanel'] is False):
return
width = shape['width'] * self.scale
height = shape['height'] * self.scale
x = top_left['x']
y = self.page_height - top_left['y'] # - height
rgb = self.get_rgb(shape['strokeColor'])
r = float(rgb[0])/255
g = float(rgb[1])/255
b = float(rgb[2])/255
self.canvas.setStrokeColorRGB(r, g, b)
stroke_width = shape.get('strokeWidth', 2)
self.canvas.setLineWidth(stroke_width)
rotation = self.panel['rotation'] * -1
if rotation != 0:
self.canvas.saveState()
self.canvas.translate(x, y)
self.canvas.rotate(rotation)
# top-left is now at 0, 0
x = 0
y = 0
self.canvas.rect(x, y, width, height * -1, stroke=1)
if rotation != 0:
# Restore coordinates, rotation etc.
self.canvas.restoreState()
def draw_line(self, shape):
start = self.panel_to_page_coords(shape['x1'], shape['y1'])
end = self.panel_to_page_coords(shape['x2'], shape['y2'])
x1 = start['x']
y1 = self.page_height - start['y']
x2 = end['x']
y2 = self.page_height - end['y']
# Don't draw if both points outside panel
if (start['inPanel'] is False) and (end['inPanel'] is False):
return
rgb = self.get_rgb(shape['strokeColor'])
r = float(rgb[0])/255
g = float(rgb[1])/255
b = float(rgb[2])/255
self.canvas.setStrokeColorRGB(r, g, b)
stroke_width = shape['strokeWidth']
self.canvas.setLineWidth(stroke_width)
p = self.canvas.beginPath()
p.moveTo(x1, y1)
p.lineTo(x2, y2)
self.canvas.drawPath(p, fill=1, stroke=1)
def draw_arrow(self, shape):
start = self.panel_to_page_coords(shape['x1'], shape['y1'])
end = self.panel_to_page_coords(shape['x2'], shape['y2'])
x1 = start['x']
y1 = self.page_height - start['y']
x2 = end['x']
y2 = self.page_height - end['y']
stroke_width = shape['strokeWidth']
# Don't draw if both points outside panel
if (start['inPanel'] is False) and (end['inPanel'] is False):
return
rgb = self.get_rgb(shape['strokeColor'])
r = float(rgb[0])/255
g = float(rgb[1])/255
b = float(rgb[2])/255
self.canvas.setStrokeColorRGB(r, g, b)
self.canvas.setFillColorRGB(r, g, b)
head_size = (stroke_width * 4) + 5
dx = x2 - x1
dy = y2 - y1
stroke_width = stroke_width * self.scale
self.canvas.setLineWidth(stroke_width)
p = self.canvas.beginPath()
f = -1
if dy == 0:
line_angle = radians(90)
if dx < 0:
f = 1
else:
line_angle = atan(dx / dy)
if dy < 0:
f = 1
# Angle of arrow head is 0.8 radians (0.4 either side of line_angle)
arrow_point1_x = x2 + (f * sin(line_angle - 0.4) * head_size)
arrow_point1_y = y2 + (f * cos(line_angle - 0.4) * head_size)
arrow_point2_x = x2 + (f * sin(line_angle + 0.4) * head_size)
arrow_point2_y = y2 + (f * cos(line_angle + 0.4) * head_size)
arrow_point_mid_x = x2 + (f * sin(line_angle) * head_size * 0.5)
arrow_point_mid_y = y2 + (f * cos(line_angle) * head_size * 0.5)
# Draw the line (at lineWidth)
p.moveTo(x1, y1)
p.lineTo(arrow_point_mid_x, arrow_point_mid_y)
self.canvas.drawPath(p, fill=1, stroke=1)
# Draw the arrow head (at lineWidth: 0)
self.canvas.setLineWidth(0)
p.moveTo(arrow_point1_x, arrow_point1_y)
p.lineTo(arrow_point2_x, arrow_point2_y)
p.lineTo(x2, y2)
p.lineTo(arrow_point1_x, arrow_point1_y)
self.canvas.drawPath(p, fill=1, stroke=1)
def draw_polygon(self, shape, closed=True):
polygon_in_viewport = False
points = []
for point in shape['points'].split(" "):
# Older polygons/polylines may be 'x,y,'
xy = point.split(",")
x = xy[0]
y = xy[1]
coords = self.panel_to_page_coords(float(x), float(y))
points.append([coords['x'], self.page_height - coords['y']])
polygon_in_viewport = polygon_in_viewport or coords['inPanel']
# Don't draw if all points outside panel viewport
if not polygon_in_viewport:
return
stroke_width = shape['strokeWidth']
rgb = self.get_rgb(shape['strokeColor'])
r = float(rgb[0])/255
g = float(rgb[1])/255
b = float(rgb[2])/255
self.canvas.setStrokeColorRGB(r, g, b)
self.canvas.setLineWidth(stroke_width)
p = self.canvas.beginPath()
# Go to start...
p.moveTo(points[0][0], points[0][1])
# ...around other points...
for point in points[1:]:
p.lineTo(point[0], point[1])
# ...and back over first line
if closed:
for point in points[0:2]:
p.lineTo(point[0], point[1])
self.canvas.drawPath(p, fill=0, stroke=1)
def draw_polyline(self, shape):
self.draw_polygon(shape, False)
def draw_ellipse(self, shape):
stroke_width = shape['strokeWidth']
c = self.panel_to_page_coords(shape['x'], shape['y'])
cx = c['x']
cy = self.page_height - c['y']
rx = shape['radiusX'] * self.scale
ry = shape['radiusY'] * self.scale
rotation = (shape['rotation'] + self.panel['rotation']) * -1
rgb = self.get_rgb(shape['strokeColor'])
r = float(rgb[0])/255
g = float(rgb[1])/255
b = float(rgb[2])/255
self.canvas.setStrokeColorRGB(r, g, b)
# Don't draw if centre outside panel
if c['inPanel'] is False:
return
# For rotation, we reset our coordinates around cx, cy
# so that rotation applies around cx, cy
self.canvas.saveState()
self.canvas.translate(cx, cy)
self.canvas.rotate(rotation)
# centre is now at 0, 0
cx = 0
cy = 0
height = ry * 2
width = rx * 2
left = cx - rx
bottom = cy - ry
# Draw ellipse...
p = self.canvas.beginPath()
self.canvas.setLineWidth(stroke_width)
p.ellipse(left, bottom, width, height)
self.canvas.drawPath(p, stroke=1)
# Restore coordinates, rotation etc.
self.canvas.restoreState()
class ShapeToPilExport(object):
"""
Class for drawing panel shapes onto a PIL image.
We get a PIL image, the panel dict, and crop coordinates
"""
def __init__(self, pil_img, panel, crop):
self.pil_img = pil_img
self.panel = panel
# The crop region on the original image coordinates...
self.crop = crop
self.scale = pil_img.size[0] / crop['width']
self.draw = ImageDraw.Draw(pil_img)
if "shapes" in panel:
for shape in panel["shapes"]:
if shape['type'] == "Arrow":
self.draw_arrow(shape)
elif shape['type'] == "Line":
self.draw_line(shape)
elif shape['type'] == "Rectangle":
self.draw_rectangle(shape)
elif shape['type'] == "Ellipse":
self.draw_ellipse(shape)
elif shape['type'] == "Polygon":
self.draw_polygon(shape)
elif shape['type'] == "Polyline":
self.draw_polyline(shape)
def get_panel_coords(self, shape_x, shape_y):
"""
Convert coordinate from the image onto the panel.
Handles zoom, offset & rotation of panel, rotating the
x, y point around the centre of the cropped region
and scaling appropriately
"""
rotation = self.panel['rotation']
if rotation != 0:
# img coords: centre of rotation
cx = self.crop['x'] + (self.crop['width']/2)
cy = self.crop['y'] + (self.crop['height']/2)
dx = cx - shape_x
dy = cy - shape_y
# distance of point from centre of rotation
h = sqrt(dx * dx + dy * dy)
# and the angle
angle1 = atan2(dx, dy)
# Add the rotation to the angle and calculate new
# opposite and adjacent lengths from centre of rotation
angle2 = angle1 - radians(rotation)
newo = sin(angle2) * h
newa = cos(angle2) * h
# to give correct x and y within cropped panel
shape_x = cx - newo
shape_y = cy - newa
# convert to coords within crop region
shape_x = (shape_x - self.crop['x']) * self.scale
shape_y = (shape_y - self.crop['y']) * self.scale
return {'x': shape_x, 'y': shape_y}
def draw_arrow(self, shape):
start = self.get_panel_coords(shape['x1'], shape['y1'])
end = self.get_panel_coords(shape['x2'], shape['y2'])
x1 = start['x']
y1 = start['y']
x2 = end['x']
y2 = end['y']
head_size = ((shape['strokeWidth'] * 4) + 5)
head_size = scale_to_export_dpi(head_size)
stroke_width = scale_to_export_dpi(shape.get('strokeWidth', 2))
rgb = ShapeToPdfExport.get_rgb(shape['strokeColor'])
# Do some trigonometry to get the line angle can calculate arrow points
dx = x2 - x1
dy = y2 - y1
if dy == 0:
line_angle = radians(90)
else:
line_angle = atan(dx / dy)
f = -1
if dy < 0:
f = 1
# Angle of arrow head is 0.8 radians (0.4 either side of line_angle)
arrow_point1_x = x2 + (f * sin(line_angle - 0.4) * head_size)
arrow_point1_y = y2 + (f * cos(line_angle - 0.4) * head_size)
arrow_point2_x = x2 + (f * sin(line_angle + 0.4) * head_size)
arrow_point2_y = y2 + (f * cos(line_angle + 0.4) * head_size)
arrow_point_mid_x = x2 + (f * sin(line_angle) * head_size * 0.5)
arrow_point_mid_y = y2 + (f * cos(line_angle) * head_size * 0.5)
points = ((x2, y2),
(arrow_point1_x, arrow_point1_y),
(arrow_point2_x, arrow_point2_y),
(x2, y2)
)
# Draw Line of arrow - to midpoint of head at full stroke width
self.draw.line([(x1, y1), (arrow_point_mid_x, arrow_point_mid_y)],
fill=rgb, width=int(stroke_width))
# Draw Arrow head, up to tip at x2, y2
self.draw.polygon(points, fill=rgb, outline=rgb)
def draw_polygon(self, shape, closed=True):
points = []
for point in shape['points'].split(" "):
# Older polygons/polylines may be 'x,y,'
xy = point.split(",")
x = xy[0]
y = xy[1]
coords = self.get_panel_coords(float(x), float(y))
points.append((coords['x'], coords['y']))
if closed:
points.append(points[0])
stroke_width = scale_to_export_dpi(shape.get('strokeWidth', 2))
rgb = ShapeToPdfExport.get_rgb(shape['strokeColor'])
# Draw all the lines (NB: polygon doesn't handle line width)
self.draw.line(points, fill=rgb, width=int(round(stroke_width)))
# Draw ellipse at each corner
# see https://stackoverflow.com/questions/33187698/
r = (stroke_width/2) * 0.9 # seems to look OK with this size
if closed:
corners = points[:]
else:
corners = points[1: -1]
for point in corners:
self.draw.ellipse((point[0] - r, point[1] - r,
point[0] + r, point[1] + r), fill=rgb)
def draw_polyline(self, shape):
self.draw_polygon(shape, False)
def draw_line(self, shape):
start = self.get_panel_coords(shape['x1'], shape['y1'])
end = self.get_panel_coords(shape['x2'], shape['y2'])
x1 = start['x']
y1 = start['y']
x2 = end['x']
y2 = end['y']
stroke_width = scale_to_export_dpi(shape.get('strokeWidth', 2))
rgb = ShapeToPdfExport.get_rgb(shape['strokeColor'])
self.draw.line([(x1, y1), (x2, y2)], fill=rgb, width=int(stroke_width))
def draw_rectangle(self, shape):
# clockwise list of corner points on the OUTSIDE of thick line
w = scale_to_export_dpi(shape.get('strokeWidth', 2))
cx = shape['x'] + (shape['width']/2)
cy = shape['y'] + (shape['height']/2)
rotation = self.panel['rotation'] * -1
# Centre of rect rotation in PIL image
centre = self.get_panel_coords(cx, cy)
cx = centre['x']
cy = centre['y']
scale_w = w
rgb = ShapeToPdfExport.get_rgb(shape['strokeColor'])
# To support rotation, draw rect on temp canvas, rotate and paste
width = int((shape['width'] * self.scale) + w)
height = int((shape['height'] * self.scale) + w)
temp_rect = Image.new('RGBA', (width, height), (255, 255, 255, 0))
rect_draw = ImageDraw.Draw(temp_rect)
# Draw outer rectangle, then remove inner rect with full opacity
rect_draw.rectangle((0, 0, width, height), fill=rgb)
rgba = (255, 255, 255, 0)
rect_draw.rectangle((scale_w, scale_w, width-scale_w, height-scale_w),
fill=rgba)
temp_rect = temp_rect.rotate(rotation, resample=Image.BICUBIC,
expand=True)
# Use rect as mask, so transparent part is not pasted
paste_x = cx - (temp_rect.size[0]/2)
paste_y = cy - (temp_rect.size[1]/2)
self.pil_img.paste(temp_rect, (int(paste_x), int(paste_y)),
mask=temp_rect)
def draw_ellipse(self, shape):
w = int(scale_to_export_dpi(shape.get('strokeWidth', 2)))
ctr = self.get_panel_coords(shape['x'], shape['y'])
cx = ctr['x']
cy = ctr['y']
rx = self.scale * shape['radiusX']
ry = self.scale * shape['radiusY']
rotation = (shape['rotation'] + self.panel['rotation']) * -1
rgb = ShapeToPdfExport.get_rgb(shape['strokeColor'])
width = int((rx * 2) + w)
height = int((ry * 2) + w)
temp_ellipse = Image.new('RGBA', (width + 1, height + 1),
(255, 255, 255, 0))
ellipse_draw = ImageDraw.Draw(temp_ellipse)
# Draw outer ellipse, then remove inner ellipse with full opacity
ellipse_draw.ellipse((0, 0, width, height), fill=rgb)
rgba = (255, 255, 255, 0)
ellipse_draw.ellipse((w, w, width - w, height - w), fill=rgba)
temp_ellipse = temp_ellipse.rotate(rotation, resample=Image.BICUBIC,
expand=True)
# Use ellipse as mask, so transparent part is not pasted
paste_x = cx - (temp_ellipse.size[0]/2)
paste_y = cy - (temp_ellipse.size[1]/2)
self.pil_img.paste(temp_ellipse, (int(paste_x), int(paste_y)),
mask=temp_ellipse)
class FigureExport(object):
"""
Super class for exporting various figures, such as PDF or TIFF etc.
"""
def __init__(self, conn, script_params, export_images=False):
self.conn = conn
self.script_params = script_params
self.export_images = export_images
self.ns = "omero.web.figure.pdf"
self.mimetype = "application/pdf"
figure_json_string = script_params['Figure_JSON']
# Since unicode can't be wrapped by rstring
figure_json_string = figure_json_string.decode('utf8')
self.figure_json = self.version_transform_json(
json.loads(figure_json_string))
n = datetime.now()
# time-stamp name by default: Figure_2013-10-29_22-43-53.pdf
self.figure_name = u"Figure_%s-%s-%s_%s-%s-%s" % (
n.year, n.month, n.day, n.hour, n.minute, n.second)
if 'figureName' in self.figure_json:
self.figure_name = self.figure_json['figureName']
# get Figure width & height...
self.page_width = self.figure_json['paper_width']
self.page_height = self.figure_json['paper_height']
def version_transform_json(self, figure_json):
v = figure_json.get('version')
if v < 3:
print "Transforming to VERSION 3"
for p in figure_json['panels']:
if p.get('export_dpi'):
# rename 'export_dpi' attr to 'min_export_dpi'
p['min_export_dpi'] = p.get('export_dpi')
del p['export_dpi']
# update strokeWidth to page pixels/coords instead of
# image pixels. Scale according to size of panel and zoom
if p.get('shapes') and len(p['shapes']) > 0:
image_pixels_width = self.get_crop_region(p)['width']
page_coords_width = float(p.get('width'))
stroke_width_scale = page_coords_width/image_pixels_width
for shape in p['shapes']:
stroke_width = shape.get('strokeWidth', 1)
stroke_width = stroke_width * stroke_width_scale
# Set stroke-width to 0.25, 0.5, 0.75, 1 or greater
if stroke_width > 0.875:
stroke_width = int(round(stroke_width))
elif stroke_width > 0.625:
stroke_width = 0.75
elif stroke_width > 0.375:
stroke_width = 0.5
else:
stroke_width = 0.25
print 'strokewidth', shape['strokeWidth'], stroke_width
shape['strokeWidth'] = stroke_width
return figure_json
def get_zip_name(self):
# file names can't include unicode characters
name = unicodedata.normalize(
'NFKD', self.figure_name).encode('ascii', 'ignore')
# in case we have path/to/name.pdf, just use name.pdf
name = path.basename(name)
# Remove commas: causes problems 'duplicate headers' in file download
name = name.replace(",", ".")
return "%s.zip" % name
def get_figure_file_name(self, page=None):
"""
For PDF export we will only create a single figure file, but
for TIFF export we may have several pages, so we need unique names
for each to avoid overwriting.
This method supports both, simply using different extension
(pdf/tiff) for each.
@param page: If we know a page number we want to use.
"""
# Extension is pdf or tiff
fext = self.get_figure_file_ext()
# file names can't include unicode characters
name = unicodedata.normalize(
'NFKD', self.figure_name).encode('ascii', 'ignore')
# in case we have path/to/name, just use name
name = path.basename(name)
# if ends with E.g. .pdf, remove extension
if name.endswith("." + fext):
name = name[0: -len("." + fext)]
# Name with extension and folder
full_name = "%s.%s" % (name, fext)
# Remove commas: causes problems 'duplicate headers' in file download
full_name = full_name.replace(",", ".")
index = page if page is not None else 1
if fext == "tiff" and self.page_count > 1:
full_name = "%s_page_%02d.%s" % (name, index, fext)
if self.zip_folder_name is not None:
full_name = os.path.join(self.zip_folder_name, full_name)
while(os.path.exists(full_name)):
index += 1
full_name = "%s_page_%02d.%s" % (name, index, fext)
if self.zip_folder_name is not None:
full_name = os.path.join(self.zip_folder_name, full_name)
# Handy to know what the last created file is:
self.figure_file_name = full_name
return full_name
def build_figure(self):
"""
The main building of the figure happens here, independently of format.
We set up directories as needed, call create_figure() to create
the PDF or TIFF then iterate through figure pages, adding panels
for each page.
Then we add an info page and create a zip of everything if needed.
Finally the created file or zip is uploaded to OMERO and attached
as a file annotation to all the images in the figure.
"""
# test to see if we've got multiple pages
page_count = ('page_count' in self.figure_json and
self.figure_json['page_count'] or 1)
self.page_count = int(page_count)
paper_spacing = ('paper_spacing' in self.figure_json and
self.figure_json['paper_spacing'] or 50)
page_col_count = ('page_col_count' in self.figure_json and
self.figure_json['page_col_count'] or 1)
# Create a zip if we have multiple TIFF pages or we're exporting Images
export_option = self.script_params['Export_Option']
create_zip = False
if self.export_images:
create_zip = True
if (self.page_count > 1) and (export_option.startswith("TIFF")):
create_zip = True
# somewhere to put PDF and images
self.zip_folder_name = None
if create_zip:
self.zip_folder_name = "figure"
curr_dir = os.getcwd()
zip_dir = os.path.join(curr_dir, self.zip_folder_name)
os.mkdir(zip_dir)
if self.export_images:
for d in (ORIGINAL_DIR, RESAMPLED_DIR, FINAL_DIR):
img_dir = os.path.join(zip_dir, d)
os.mkdir(img_dir)
self.add_read_me_file()
# Create the figure file(s)
self.create_figure()
panels_json = self.figure_json['panels']
image_ids = set()
group_id = None
# We get our group from the first image
id1 = panels_json[0]['imageId']
group_id = self.conn.getObject("Image", id1).getDetails().group.id.val
# For each page, add panels...
col = 0
row = 0
for p in range(self.page_count):
self.add_page_color()
px = col * (self.page_width + paper_spacing)
py = row * (self.page_height + paper_spacing)
page = {'x': px, 'y': py}
self.add_panels_to_page(panels_json, image_ids, page)
# complete page and save
self.save_page(p)
col = col + 1
if col >= page_col_count:
col = 0
row = row + 1
# Add thumbnails and links page
self.add_info_page(panels_json)
# Saves the completed figure file
self.save_figure()
return
# # PDF will get created in this group
# if group_id is None:
# group_id = self.conn.getEventContext().groupId
# self.conn.SERVICE_OPTS.setOmeroGroup(group_id)
# return self.create_file_annotation(image_ids)
def create_file_annotation(self, image_ids):
output_file = self.figure_file_name
ns = self.ns
mimetype = self.mimetype
if self.zip_folder_name is not None:
zip_name = self.get_zip_name()
# Recursively zip everything up
compress(zip_name, self.zip_folder_name)
output_file = zip_name
ns = "omero.web.figure.zip"
mimetype = "application/zip"
file_ann = self.conn.createFileAnnfromLocalFile(
output_file,
mimetype=mimetype,
ns=ns)
links = []
for iid in list(image_ids):
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = file_ann._obj
links.append(link)
if len(links) > 0:
# Don't want to fail at this point due to strange permissions combo
try:
links = self.conn.getUpdateService().saveAndReturnArray(
links, self.conn.SERVICE_OPTS)
except Exception:
logger.error("Failed to attach figure: %s to images %s"
% (file_ann, image_ids))
return file_ann
def apply_rdefs(self, image, channels):
""" Apply the channel levels and colors to the image """
c_idxs = []
windows = []
colors = []
reverses = []
# OMERO.figure doesn't support greyscale rendering
image.setColorRenderingModel()
for i, c in enumerate(channels):
if c['active']:
c_idxs.append(i+1)
windows.append([c['window']['start'], c['window']['end']])
colors.append(c['color'])
reverses.append(c.get('reverseIntensity', False))
image.setActiveChannels(c_idxs, windows, colors, reverses)
def get_crop_region(self, panel):
"""
Gets the width and height in points/pixels for a panel in the
figure. This is at the 'original' figure / PDF coordinates
(E.g. before scaling for TIFF export)
"""
zoom = float(panel['zoom'])
frame_w = panel['width']
frame_h = panel['height']
dx = panel.get('dx', DEFAULT_OFFSET)
dy = panel.get('dy', DEFAULT_OFFSET)
orig_w = panel['orig_width']
orig_h = panel['orig_height']
# need tile_x, tile_y, tile_w, tile_h
tile_w = orig_w / (zoom/100)
tile_h = orig_h / (zoom/100)
orig_ratio = float(orig_w) / orig_h
wh = float(frame_w) / frame_h
if abs(orig_ratio - wh) > 0.01:
# if viewport is wider than orig...
if (orig_ratio < wh):
tile_h = tile_w / wh
else:
tile_w = tile_h * wh
cropx = ((orig_w - tile_w)/2) - dx
cropy = ((orig_h - tile_h)/2) - dy
return {'x': cropx, 'y': cropy, 'width': tile_w, 'height': tile_h}
def get_time_label_text(self, delta_t, format):
""" Gets the text for 'live' time-stamp labels """
# format of "secs" by default
text = "%s secs" % delta_t
if format == "mins":
text = "%s mins" % int(round(float(delta_t) / 60))
elif format == "hrs:mins":
h = (delta_t / 3600)
m = int(round((float(delta_t) % 3600) / 60))
text = "%s:%02d" % (h, m)
elif format == "hrs:mins:secs":
h = (delta_t / 3600)
m = (delta_t % 3600) / 60
s = delta_t % 60
text = "%s:%02d:%02d" % (h, m, s)
return text
def add_rois(self, panel, page):
"""
Add any Shapes
"""
if "shapes" not in panel:
return
crop = self.get_crop_region(panel)
ShapeToPdfExport(self.figure_canvas, panel, page, crop,
self.page_height)
def draw_labels(self, panel, page):
"""
Add the panel labels to the page.
Here we calculate the position of labels but delegate
to self.draw_text() to actually place the labels on PDF/TIFF
"""
labels = panel['labels']
x = panel['x']
y = panel['y']
width = panel['width']
height = panel['height']
# Handle page offsets
x = x - page['x']
y = y - page['y']
spacer = 5
# group by 'position':
positions = {'top': [], 'bottom': [], 'left': [],
'leftvert': [], 'right': [],
'topleft': [], 'topright': [],
'bottomleft': [], 'bottomright': []}
for l in labels:
if 'text' not in l:
the_t = panel['theT']
timestamps = panel.get('deltaT')
if l.get('time') == "index":
l['text'] = str(the_t + 1)
elif timestamps and panel['theT'] < len(timestamps):
d_t = panel['deltaT'][the_t]
l['text'] = self.get_time_label_text(d_t, l['time'])
else:
continue
pos = l['position']
l['size'] = int(l['size']) # make sure 'size' is number
# If page is black and label is black, make label white
page_color = self.figure_json.get('page_color', 'ffffff').lower()
label_color = l['color'].lower()
label_on_page = pos in ('left', 'right', 'top',
'bottom', 'leftvert')
if label_on_page:
if label_color == '000000' and page_color == '000000':
l['color'] = 'ffffff'
if label_color == 'ffffff' and page_color == 'ffffff':
l['color'] = '000000'
if pos in positions:
positions[pos].append(l)
def draw_lab(label, lx, ly, align='left'):
label_h = label['size']
color = label['color']
red = int(color[0:2], 16)
green = int(color[2:4], 16)
blue = int(color[4:6], 16)
fontsize = label['size']
rgb = (red, green, blue)