def color_tiles(img):
size = img.size
small_img = img.resize((size[0]/2, size[1]/2), BILINEAR)
bw_img = small_img.convert('1', dither=False)
gray_img = bw_img.convert('L')
result = Image.new('RGB', size)
tile1 = ImageOps.colorize(gray_img, 'green', 'red')
tile2 = ImageOps.colorize(gray_img, 'purple', 'yellow')
tile3 = ImageOps.colorize(gray_img, 'yellow', 'brown')
tile4 = ImageOps.colorize(gray_img, 'red', 'cyan')
result.paste(tile1, (0, 0))
result.paste(tile2, (size[0]/2, 0))
result.paste(tile3, (0, size[1]/2))
result.paste(tile4, (size[0]/2, size[1]/2))
return result
def color_tiles(img):
size = img.size
small_img = img.resize((size[0] / 2, size[1] / 2), BILINEAR)
bw_img = small_img.convert('1', dither=False)
gray_img = bw_img.convert('L')
result = Image.new('RGB', size)
tile1 = ImageOps.colorize(gray_img, 'green', 'red')
tile2 = ImageOps.colorize(gray_img, 'purple', 'yellow')
tile3 = ImageOps.colorize(gray_img, 'yellow', 'brown')
tile4 = ImageOps.colorize(gray_img, 'red', 'cyan')
result.paste(tile1, (0, 0))
result.paste(tile2, (size[0] / 2, 0))
result.paste(tile3, (0, size[1] / 2))
result.paste(tile4, (size[0] / 2, size[1] / 2))
return result
def tats(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 9)
colours = util.order_colours_by_brightness(colours)
bg = random.choice(colours[:3])
light = random.choice(colours[3:6])
dark = random.choice(colours[6:])
dist = math.sqrt(sum(map(lambda (a, b): math.pow(a - b, 2), zip(light, dark))))
if dist < 100:
light = util.modify_hls(light, l=lambda l: l + 100)
light = util.modify_hls(light, s=lambda s: s + 100)
dark = util.modify_hls(dark, s=lambda s: s + 100)
layer = Image.open(os.path.dirname(os.path.abspath(__file__)) + '/' +
'assets/tats.png')
layer.load()
r, g, b, a = layer.split()
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, tuple(dark), tuple(light))
layer.putalpha(a)
im = Image.new('RGB', layer.size, tuple(bg))
im.paste(layer, mask=layer)
return im
def put_contour(image,
size=1,
offset=0,
contour_color=0,
fill_color=0,
opacity=100,
include_image=True):
if not has_transparency(image):
return put_border(image, size, offset, contour_color, fill_color,
opacity, include_image)
image = image.convert('RGBA')
mask = imtools.get_alpha(image)
w, h = image.size
outer_mask = mask.resize(
(w + 2 * (size + offset), h + 2 * (size + offset)), Image.ANTIALIAS)
inner_mask = mask.resize((w + 2 * offset, h + 2 * offset), Image.ANTIALIAS)
inner_mask = ImageOps.expand(inner_mask, border=size, fill=0)
paste(outer_mask, (255 * opacity) / 100, mask=inner_mask)
if include_image:
image = ImageOps.expand(image, border=size + offset, fill=(0, 0, 0, 0))
mask = ImageOps.expand(mask, border=size + offset, fill=0)
paste(outer_mask, 255, mask=mask)
contour = ImageOps.colorize(outer_mask, (255, 255, 255), contour_color)
paste(contour, fill_color, mask=inner_mask)
if include_image:
paste(contour, image, mask=image)
contour.putalpha(outer_mask)
return contour
def put_contour(image, size=1, offset=0, contour_color=0, fill_color=0,
opacity=100, include_image=True):
if not has_transparency(image):
return put_border(
image, size, offset, contour_color, fill_color,
opacity, include_image)
image = image.convert('RGBA')
mask = imtools.get_alpha(image)
w, h = image.size
outer_mask = mask.resize(
(w + 2 * (size + offset), h + 2 * (size + offset)),
Image.ANTIALIAS)
inner_mask = mask.resize(
(w + 2 * offset, h + 2 * offset),
Image.ANTIALIAS)
inner_mask = ImageOps.expand(inner_mask, border=size, fill=0)
paste(outer_mask, (255 * opacity) / 100, mask=inner_mask)
if include_image:
image = ImageOps.expand(image, border=size + offset, fill=(0, 0, 0, 0))
mask = ImageOps.expand(mask, border=size + offset, fill=0)
paste(outer_mask, 255, mask=mask)
contour = ImageOps.colorize(outer_mask, (255, 255, 255), contour_color)
paste(contour, fill_color, mask=inner_mask)
if include_image:
paste(contour, image, mask=image)
contour.putalpha(outer_mask)
return contour
def rotate_and_draw_date(img, x_position, row_y, current_day, color):
font = ImageFont.truetype("arial.ttf", 14)
txt = Image.new('L', (100, 25))
d = ImageDraw.Draw(txt)
d.text((0, 0), current_day.__str__(), font=font, fill=255)
w = txt.rotate(-90, expand=1)
img.paste(ImageOps.colorize(w, (0, 0, 0), color), (x_position, row_y), w)
def run(self):
'''
Limpia las imagenes empleando PIL
'''
# notificar el inicio de operaciones
self.notificador.inicio_operacion.emit()
import Image, ImageChops, ImageOps, ImageEnhance
for i in range(len(self.imagenesIn)):
im = Image.open(self.imagenesIn[i])
if im:
im1 = ImageChops.invert(im)
im = ImageChops.subtract(im1, im)
im = im.convert('L')
im = ImageChops.invert(im)
im = ImageEnhance.Brightness(im).enhance(2.0)
im = ImageOps.colorize(im, (0, 0, 0), (255, 255, 255))
im.save(self.imagenesOut[i])
else:
self.notificador.error.emit('Error al procesar la imagen: ' +
self.imagenesIn[i])
return
# notificar a la aplicacion el resultado de la operacion
self.notificador.correcto.emit(self.plugin.nombre())
# notificar el fin de operaciones
self.notificador.fin_operacion.emit()
return
def tats(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 9)
colours = util.order_colours_by_brightness(colours)
bg = random.choice(colours[:3])
light = random.choice(colours[3:6])
dark = random.choice(colours[6:])
dist = math.sqrt(
sum(map(lambda (a, b): math.pow(a - b, 2), zip(light, dark))))
if dist < 100:
light = util.modify_hls(light, l=lambda l: l + 100)
light = util.modify_hls(light, s=lambda s: s + 100)
dark = util.modify_hls(dark, s=lambda s: s + 100)
layer = Image.open(
os.path.dirname(os.path.abspath(__file__)) + '/' + 'assets/tats.png')
layer.load()
r, g, b, a = layer.split()
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, tuple(dark), tuple(light))
layer.putalpha(a)
im = Image.new('RGB', layer.size, tuple(bg))
im.paste(layer, mask=layer)
return im
def cf_image(cfs, coords, width=None, height=None, pos=(0,0),
size=26, border=5, bg=(0,0,0), colmap=None):
"""
Returns a PIL image showing the selected connection fields (CFS)
as supplied by extract_CFs. Does not support non-square CF
shapes.
'cfs' is an ndarray of N dstacked cfs, each of shape (X,X): (X,X,N)
'coords' is an ndarray of N coordinates: (N,2)
'width' and 'height' are either None (full) of integer grid sizes
'pos' is the starting position of the block, (x,y)
'size' and 'border' are the cf image size and the border size in pixels.
'colmap' is an RGB array shape (N,M,3) with values between 0.0 and 1.0.
"""
normalize = lambda arr: (arr - arr.min()) / (arr.max() - arr.min())
cf_im = lambda cf, size: greyscale(normalize(cf)).resize((size,size),
Image.NEAREST)
(posx, posy) = pos
(d1,d2) = zip(*coords)
density = len(set(d1))
assert density == len(set(d2)), "Not implemented for non-square sets"
height = density if height is None else height
width = density if width is None else width
assert height>0 and width>0, "Height and width must be None or greater than zero"
assert posx+width <= density, "X position and width greater than density"
assert posy+height <= density, "Y position and width greater than density"
# Functions mapping original coordinates onto consecutive grid indices
fst_map = dict(((ind,i) for (i,ind) in enumerate(sorted(set(d1)))))
snd_map = dict(((ind,i) for (i,ind) in enumerate(sorted(set(d2)))))
# Generating a dictionary from the grid coordinates to the CF index
mapped_coords = [(fst_map[fst],snd_map[snd]) for [fst,snd] in coords]
indexed_coords = dict((coord,i) for (i, coord) in enumerate(mapped_coords))
# Initialising the image
imwidth = width*size+(width-1)*border
imheight = height*size+(height-1)*border
cf_block = Image.new('RGB', (imwidth, imheight), bg)
# Building image row by row, top to bottom.
for yind in range(height):
for xind in range(width):
# Swapped coordinate system
cf_ind = indexed_coords[(yind+posy, xind+posx)]
# Get color from the color map if available
if colmap is not None:
crd1, crd2 = coords[cf_ind]
r,g,b = colmap[crd1, crd2, :]
color = (r*255,g*255,b*255)
else:
color = (255, 255, 255)
cf = cfs[:,:,cf_ind]
(cf_dim1, cf_dim2) = cf.shape
assert cf_dim1 == cf_dim2, "Only supports square CFs."
cf_image = ImageOps.colorize(cf_im(cf, size), (0, 0, 0, 0), color)
xoffset = xind*border
yoffset = yind*border
paste_coord = (xoffset+xind*size, yoffset+yind*size)
cf_block.paste(cf_image, paste_coord)
return cf_block
def triangles(original, n=30, size=150, width=700,
height=700, min_distance=70, opacity=220):
original = original.convert('RGB')
colours = util.get_dominant_colours(original, 8)
colours_ordered = util.order_colours_by_brightness(colours)
brightest_colour = list(random.choice(colours_ordered[:3]))
brightest_colour.append(0)
new = Image.new('RGBA', (width, height), tuple(brightest_colour))
draw = aggdraw.Draw(new)
centres = []
def is_too_close(x, y):
for centre in centres:
if math.sqrt(math.pow(centre[0] - x, 2) +
math.pow(centre[1] - y, 2)) < min_distance:
return True
return False
for i in xrange(n):
colour = tuple(colours[int(random.randint(0, len(colours) - 1))])
x = random.randint(size / 2, width - 1 - size / 2)
y = random.randint(size / 2, height - 1 - size / 2)
if is_too_close(x, y):
continue
centres.append((x, y))
brush = aggdraw.Brush(colour, opacity)
points = get_triangle_path(x, y, size / 2, size / 2)
draw.polygon(points, None, brush)
draw.flush()
brightest_colour = brightest_colour[0:3]
texture = Image.open(os.path.dirname(os.path.abspath(__file__)) + '/' +
'assets/airbrush.png')
texture = texture.convert('RGBA')
r, g, b, a = texture.split()
texture = ImageOps.grayscale(texture)
texture = ImageOps.colorize(texture, (0, 0, 0), tuple(brightest_colour))
texture = texture.convert('RGBA')
texture.putalpha(a)
r, g, b, a = new.split()
texture = texture.crop((0, 0, width, height))
texture_layer = Image.new('RGBA', (width, height), (0, 0, 0, 0))
texture_layer.paste(texture, mask=new)
new.paste(texture_layer, mask=texture_layer)
im = Image.new('RGB', (width, height), tuple(brightest_colour))
im.paste(new, mask=a)
return im
def changeColor(self, image, mask, color1, color2=(0, 0, 0, 0)):
"""Take an image and change its color, color is a tuple (R,G,B)"""
print 'changing color of image to (%i, %i, %i, %i)' % color1
self.imageAttr(image)
image = ImageOps.colorize(image, color1, color2)
xsize, ysize = image.size
blank = Image.open('%s%i.png' % (self.templatePath, xsize))
mask = Image.open(mask)
image = Image.composite(image, blank, mask)
return image
def colorize_pixbuf (pixbuf, black, white):
i = pixbuf_to_pil(pixbuf)
i.save('/tmp/test_pb.png','png')
irgb = Image.open('/tmp/test_pb.png')
irgb.save('/tmp/test_rgb.png','png')
ig = irgb.convert('L')
ig.save('/tmp/test_L.png','png')
icol = ImageOps.colorize(ig,black,white)
icol.save('/tmp/test.png','png')
return pil_to_pixbuf(icol)
def colorize(image, black, white, amount=100):
"""Apply a filter
- amount: 0-1"""
if image.mode != 'L':
im = image.convert('L')
else:
im = image
colorized = ImageOps.colorize(im, black, white)
if image.mode == 'RGBA':
colorized = colorized.convert('RGBA')
colorized.putalpha(imtools.get_alpha(image))
if amount < 100:
return imtools.blend(image, colorized, amount / 100.0)
return colorized
def colorize(image, black, white, amount=100):
"""Apply a filter
- amount: 0-1"""
if image.mode != 'L':
im = image.convert('L')
else:
im = image
colorized = ImageOps.colorize(im, black, white)
if image.mode == 'RGBA':
colorized = colorized.convert('RGBA')
colorized.putalpha(imtools.get_alpha(image))
if amount < 100:
return imtools.blend(image, colorized, amount / 100.0)
return colorized
def ombre(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 12)
colours = util.order_colours_by_brightness(colours)
light = random.choice(colours[:3])
dark = random.choice(colours[-3:])
layer = Image.open(
os.path.dirname(os.path.abspath(__file__)) + '/' + 'assets/ombre.jpg')
layer = util.random_crop(layer, util.WIDTH, util.HEIGHT)
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, dark, light)
return layer
def ombre(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 12)
colours = util.order_colours_by_brightness(colours)
light = random.choice(colours[:3])
dark = random.choice(colours[-3:])
layer = Image.open(os.path.dirname(os.path.abspath(__file__)) + '/' +
'assets/ombre.jpg')
layer = util.random_crop(layer, util.WIDTH, util.HEIGHT)
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, dark, light)
return layer
def mkImage (f, s, r):
img = Image.new("RGB", (28,28), "#FFFFFF");
#draw = ImageDraw.Draw(image);
font = ImageFont.truetype(f, 32);
t = Image.new('L', (100,100));
d = ImageDraw.Draw(t);
size = d.textsize(s, font=font);
d.text((50,55), " "+s+" ", font=font, fill=255);
t = t.rotate(r, expand=1);
xsum = 0;
ysum = 0;
minx = 100;
miny = 100;
maxx = 0;
maxy = 0;
pixcount = 0;
for i in range (0,t.size[0]):
for j in range (0, t.size[1]):
if (t.getpixel((i,j)) > 200):
if ( minx > i ): minx = i;
if ( miny > j ): miny = j;
if ( maxx < i ): maxx = i;
if ( maxy < j ): maxy = j;
t.putpixel((i,j), 255);
xsum += i;
ysum += j;
pixcount += 1;
# xavr = xsum / (pixcount);
# yavr = ysum / (pixcount);
midx = (minx + maxx)/2;
midy = (miny + maxy)/2;
# if ( pixcount == 0 ):
# print "pixcount == 0 at ", f, s;
#d.text((14-size[0]/2,14-size[1]/2), s, font=font, fill=255);
#img.paste(t, (0,0,t.size[0],t.size[1]));
img.paste(ImageOps.colorize(t,(0,0,0),(0,0,0)), (14-midx,14-midy),t);
return img;
def render(self,im):
im2 = im.copy()
if self.grayscale:
im2 = ImageOps.grayscale(im2)
im2 = ImageOps.colorize(im2,"black","white")
if self.posterized:
im2 = ImageOps.autocontrast(im2)
im2 = ImageOps.posterize(im2,self.posterize_bits)
im2 = ImageOps.autocontrast(im2)
if self.gridlines > 0:
im2 = draw_grid(im2,self.gridlines)
data = im2.tostring()
surface = pygame.image.fromstring(data, im2.size, im2.mode)
screen.blit(surface,(0,0))
pygame.display.flip()
def process_bmp ( Data):
Size = [0,0]
Size[0] = ord(Data[0]) | (ord(Data[1]) << 8)
Size[1] = ord(Data[2]) | (ord(Data[3]) << 8)
Im = Image.fromstring( "1", (Size[1], Size[0]), Data[4:], "raw", "1;IR", 0, 1)
Im = Im.rotate(90).transpose(Image.FLIP_TOP_BOTTOM).convert('L')
Im = ImageOps.colorize( Im, LCD_CHAR_COLOR, LCD_BACKLIGHT_COLOR)
Size = (Im.size[0] + BORD_W*2, Im.size[1] + BORD_W*2) # Add space for border
newIm = Image.new( 'RGBA', Size)
newIm.paste( Im, (1,1))
del Im
Draw = ImageDraw.Draw(newIm)
Draw.rectangle([(0,0), (Size[0] - 1, Size[1] - 1)], outline = BORD_COLOR)
del Draw
return newIm
def load_images(self):
self.puff_images = {}
for color in self.colors:
p_color = ui.parse_color(color)
self.puff_images[p_color] = []
for i in range(25):
with io.BytesIO(
ui.Image(self.puff_image_name +
str(i).zfill(2)).to_png()) as fp:
orig_puff = pilImage.open(fp)
gray_img = orig_puff.convert('L')
color_puff = ImageOps.colorize(gray_img, 'black', color)
with io.BytesIO() as fp2:
color_puff.save(fp2, 'PNG')
self.puff_images[p_color].append(
ui.Image.from_data(fp2.getvalue()))
def bokeh(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 8)
colours = util.order_colours_by_brightness(colours)[2:7]
colour = random.choice(colours)
colour = util.modify_hsv(colour, s=lambda s: 255, v=lambda v: 255)
light = (255, 244, 180)
layer = Image.open(os.path.dirname(os.path.abspath(__file__)) + '/' +
'assets/bokeh.png')
layer = util.random_crop(layer, util.WIDTH, util.HEIGHT)
r, g, b, a = layer.split()
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, colour, light)
layer.putalpha(a)
im = Image.new('RGB', layer.size)
im.paste(layer, (0, 0), layer)
return im
def plaid(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 12)
colours = util.order_colours_by_brightness(colours)
indices = sorted(random.sample(range(len(colours)), 3))
colours = [colours[i] for i in indices]
light, bg, dark = map(tuple, colours)
layer = Image.open(
os.path.dirname(os.path.abspath(__file__)) + '/' + 'assets/plaid.png')
layer.load()
r, g, b, a = layer.split()
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, dark, light)
layer.putalpha(a)
im = Image.new('RGB', layer.size, bg)
im.paste(layer, mask=layer)
return im
def bokeh(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 8)
colours = util.order_colours_by_brightness(colours)[2:7]
colour = random.choice(colours)
colour = util.modify_hsv(colour, s=lambda s: 255, v=lambda v: 255)
light = (255, 244, 180)
layer = Image.open(
os.path.dirname(os.path.abspath(__file__)) + '/' + 'assets/bokeh.png')
layer = util.random_crop(layer, util.WIDTH, util.HEIGHT)
r, g, b, a = layer.split()
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, colour, light)
layer.putalpha(a)
im = Image.new('RGB', layer.size)
im.paste(layer, (0, 0), layer)
return im
def draw(**kw):
shape_size = 50, 90
space = shape_size[0]//3
margin = 10
card = Image.new( 'RGB', ((shape_size[0]*3)+((margin+space)*2),
shape_size[1] + (margin * 2) ), 'white' )
if not os.path.isfile('shapes.png') \
or Image.open('shapes.png').size != (shape_size[0]*3, shape_size[1]*3):
#print "regenerating shapes.png... please stand by"
create('shapes.png', shape_size)
try:
number = Card.numbers.index(kw['number']) + 1
x1 = Card.shades.index(kw['shade']) * shape_size[0]
x2 = x1 + shape_size[0]
y1 = Card.shapes.index(kw['shape']) * shape_size[1]
y2 = y1 + shape_size[1]
shapes = Image.open('shapes.png')
shape = shapes.crop( (x1,y1,x2,y2) )
im = Image.new( 'L', (number*(shape_size[0]+space)-space, shape_size[1]), 'white' )
for n in xrange(number):
a = (shape_size[0]+space) * n
b = a + shape_size[0]
box = (a, 0, b, shape_size[1])
im.paste(shape, box)
im = ImageOps.colorize(im, kw['color'], 'white')
card.paste(im, center(im, card.size))
except Exception as e:
draw = ImageDraw.Draw(card)
error = traceback.format_exc()
attributes = ' '.join(kw.values())
for n, errLine in enumerate([attributes] + error.split('\n')):
draw.text((0,15*n), errLine, fill='black')
#card.show()
ret = cStringIO.StringIO()
card.save(ret, 'PNG')
return ret
def plaid(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 12)
colours = util.order_colours_by_brightness(colours)
indices = sorted(random.sample(range(len(colours)), 3))
colours = [colours[i] for i in indices]
light, bg, dark = map(tuple, colours)
layer = Image.open(os.path.dirname(os.path.abspath(__file__)) + '/' +
'assets/plaid.png')
layer.load()
r, g, b, a = layer.split()
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, dark, light)
layer.putalpha(a)
im = Image.new('RGB', layer.size, bg)
im.paste(layer, mask=layer)
return im
def topics2image2(ar, zoom = 1):
square_size = int(math.sqrt(len(ar[0])))
topics = Image.new("L", ((square_size*zoom+5)* len(ar), square_size*zoom+10),200)
imzoom = numpy.ones((zoom,zoom), numpy.uint8)
maxval = numpy.ones(square_size)
for topic in range(len(ar)):
pixels = numpy.zeros((square_size,square_size), numpy.uint8)
for i in range(square_size):
pixels[i,:] = map(lambda x:255*x, ar[topic][i*square_size:(i+1)*square_size ])
#print pixels
pixels = numpy.kron(pixels, imzoom)
pixels = (255 - pixels)
img = Image.fromarray(pixels,"L")#.convert("RGB")
# img = ImageOps.convert(img)
img = ImageOps.autocontrast(img)
img = ImageOps.colorize(img, (0,0,0), (255,255,255))
topics.paste(img, (1+(square_size*zoom+5)*topic, 5))
return topics
def leaves(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 8)
light, dark = [colours[i] for i in random.sample(range(len(colours)), 2)]
layer = Image.open(
os.path.dirname(os.path.abspath(__file__)) + '/' + 'assets/leaves.png')
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, dark, light)
width, height = layer.size
# shift half of the image horizontally
left = layer.crop((0, 0, width / 2, height))
right = layer.crop((width / 2, 0, width, height))
new = Image.new('RGB', (width, height))
new.paste(left, (width / 2, 0))
new.paste(right, (0, 0))
return new
def leaves(image):
image = image.convert('RGB')
colours = util.get_dominant_colours(image, 8)
light, dark = [colours[i] for i in random.sample(range(len(colours)), 2)]
layer = Image.open(os.path.dirname(os.path.abspath(__file__)) + '/' +
'assets/leaves.png')
layer = layer.convert('RGB')
layer = ImageOps.grayscale(layer)
layer = ImageOps.colorize(layer, dark, light)
width, height = layer.size
# shift half of the image horizontally
left = layer.crop((0, 0, width / 2, height))
right = layer.crop((width / 2, 0, width, height))
new = Image.new('RGB', (width, height))
new.paste(left, (width / 2, 0))
new.paste(right, (0, 0))
return new
def topics2image2(ar, zoom=1):
square_size = int(math.sqrt(len(ar[0])))
topics = Image.new(
"L", ((square_size * zoom + 5) * len(ar), square_size * zoom + 10),
200)
imzoom = numpy.ones((zoom, zoom), numpy.uint8)
maxval = numpy.ones(square_size)
for topic in range(len(ar)):
pixels = numpy.zeros((square_size, square_size), numpy.uint8)
for i in range(square_size):
pixels[i, :] = map(
lambda x: 255 * x,
ar[topic][i * square_size:(i + 1) * square_size])
#print pixels
pixels = numpy.kron(pixels, imzoom)
pixels = (255 - pixels)
img = Image.fromarray(pixels, "L") #.convert("RGB")
# img = ImageOps.convert(img)
img = ImageOps.autocontrast(img)
img = ImageOps.colorize(img, (0, 0, 0), (255, 255, 255))
topics.paste(img, (1 + (square_size * zoom + 5) * topic, 5))
return topics
def makecolourediconset(shape, icon_colours, bg):
coloured_images = []
for col in icon_colours:
coloured_images.append(ImageOps.colorize(shape, col, bg))
coloured_images.append(ImageOps.colorize(shape, bg, bg))
return coloured_images
def mkImage (f, s, r):
img = Image.new("RGB", (28,28), "#FFFFFF");
#draw = ImageDraw.Draw(image);
minx = 100;
miny = 100;
maxx = 0;
maxy = 0;
t = Image.new('L', (100,100));
for fontsize in range(1,9):
font = ImageFont.truetype(f, 16+fontsize*5);
t = Image.new('L', (500,500));
d = ImageDraw.Draw(t);
size = d.textsize(s, font=font);
d.text((50,50), " "+s+" ", font=font, fill=255);
t = t.rotate(r, expand=1);
#xsum = 0;
#ysum = 0;
minx = 100000;
miny = 100000;
maxx = 0;
maxy = 0;
#pixcount = 0;
for i in range (0,t.size[0]):
for j in range (0, t.size[1]):
if (t.getpixel((i,j)) > 100):
if ( minx > i ): minx = i;
if ( miny > j ): miny = j;
if ( maxx < i ): maxx = i;
if ( maxy < j ): maxy = j;
t.putpixel((i,j), 255);
#xsum += i;
#ysum += j;
#pixcount += 1;
xwidth = maxx-minx;
ywidth = maxy-miny;
# print minx, maxx, miny, maxy
if ( xwidth > 18 and xwidth < 28): break;
if ( ywidth > 18 and ywidth < 28): break;
# xavr = xsum / (pixcount);
# yavr = ysum / (pixcount);
midx = (minx + maxx)/2;
midy = (miny + maxy)/2;
print minx, maxx, miny, maxy, midx, midy
# if ( pixcount == 0 ):
# print "pixcount == 0 at ", f, s;
#d.text((14-size[0]/2,14-size[1]/2), s, font=font, fill=255);
#img.paste(t, (0,0,t.size[0],t.size[1]));
img.paste(ImageOps.colorize(t,(0,0,0),(0,0,0)), (14-midx,14-midy),t);
return img;
def vdiff(im0, im1):
im0 = ImageOps.colorize( im0.convert('L'), (255, 0, 0), (255, 255, 255))
im1 = ImageOps.colorize( im1.convert('L'), (0, 255, 0), (255, 255, 255))
ImageChops.multiply(im0, im1).show()
def counting(c_std, a_std, imageFile):
image_list = [imageFile]
c_std = float(c_std)
if image_list[0][-3:] == 'tif':
for f, filename in enumerate(image_list):
subprocess.call(["convert", filename, filename + '.png'])
image_list[f] = filename + '.png'
output_filename_hash = (datetime.datetime.now().minute * 60 +
datetime.datetime.now().second)
images = [
scipy.misc.imread(filename).astype(np.uint16)
for filename in image_list
]
#correlation_matrix = np.array([[-1, -1, -1, -1, -1],
# [-1, -1, -1, -1, -1],
# [-1, -1, 24, -1, -1],
# [-1, -1, -1, -1, -1],
# [-1, -1, -1, -1, -1]])
correlation_matrix = np.array([[-5935, -5935, -5935, -5935, -5935],
[-5935, 8027, 8027, 8027, -5935],
[-5935, 8027, 30742, 8027, -5935],
[-5935, 8027, 8027, 8027, -5935],
[-5935, -5935, -5935, -5935, -5935]])
median_diameter = 5
local_max = 3
#c_std = 1
processed_images = [np.copy(image).astype(np.int64) for image in images]
processed_images = \
[np.subtract(image, np.minimum(spf.median_filter(image, median_diameter),
image))
for image in images]
processed_images = \
[np.maximum(scipy.signal.correlate(image, correlation_matrix, mode='same'),
np.zeros_like(image)).astype(np.int64)
for image in processed_images]
thresholded_images = [
image > np.mean(image) + c_std * np.std(image)
#images[i] > np.mean(images[i]) + a_std * np.std(images[i])
#images[i] > a_std
for i, image in enumerate(processed_images)
]
for i, mask in enumerate(thresholded_images):
for (h, w), valid in np.ndenumerate(mask):
if valid:
local_slice = \
np.copy(processed_images[i][h - local_max:h + local_max + 1,
w - local_max:w + local_max + 1])
if (h + local_max >= mask.shape[0]
or w + local_max >= mask.shape[1] or h - local_max < 0
or w - local_max < 0):
mask[h, w] = False
continue
local_slice[local_max, local_max] = 0
if np.amax(local_slice) >= processed_images[i][h, w]:
mask[h, w] = False
size = 4
for i, image in enumerate(images):
i_std = np.std(image)
i_median = np.median(image) - i_std
i_max = np.amax(image)
for (h, w), value in np.ndenumerate(image):
if image[h, w] > i_median:
image[h, w] = int(
np.around(
math.sqrt(image[h, w] - i_median) /
math.sqrt(i_max - i_median) * float(2**8 - 1)))
else:
image[h, w] = 0
output_images = [
ImageOps.colorize(
Image.fromstring('L', image.shape, image.astype(np.uint8)),
(0, 0, 0), (255, 255, 255)) for image in images
]
for i, image in enumerate(images):
for (h, w), value in np.ndenumerate(image):
if thresholded_images[i][h, w]:
box = ((w - size, h - size), (w + size, h + size))
draw = ImageDraw.Draw(output_images[i])
draw.rectangle(box, fill=None, outline='blue')
# Editing the output file name; Will have the same as the filename + png
[
image.save(
str(i).zfill(int(np.ceil(math.log(len(output_images), 10)))) +
' SIMPLE ' + str(output_filename_hash) + '.png')
for i, image in enumerate(output_images)
]
for i, image in enumerate(thresholded_images):
print(
str(i).zfill(int(np.ceil(math.log(len(thresholded_images), 10)))) +
' ' + str(np.sum(np.sum(image))))
return 5 + ulpaste[1] + im.size[1] - slotwidth * (i + 1)
for i in xrange(slots):
draw.text((ulpaste[0] - 6 * slotwidth, getrow(i)),
"0x%08x" % (i * 0x02000000),
fill="#444444",
font=dpf)
for row in xrange(32):
txt = Image.new("L", (600, 60))
d = ImageDraw.Draw(txt)
d.text((0, 0), "0x%08x" % (row * 0x00100000), fill=255, font=dpf)
del d
rtxt = txt.rotate(17.5, expand=1)
fim.paste(ImageOps.colorize(rtxt, "#ffffff", "#444444"),
(ulpaste[0] +
(row * (p_per_col / 32) * pheight), ulpaste[1] - 4 * slotwidth),
rtxt)
del txt
del rtxt
#draw.text ((ulpaste[0] + 0x00011000 * p_per_col*pheight / (32*1024*1024), ulpaste[1] + 65*slotwidth),
# "Code/Data", fill="#000000", font=dpf)
#draw.text ((ulpaste[0] + 0x018C0000 * p_per_col*pheight / (32*1024*1024), ulpaste[1] + 65*slotwidth),
# "Stack/Heap", fill="#000000", font=dpf)
def writerow(i, str):
draw.text((10 * slotwidth, getrow(i)), str, fill="#000000", font=dpf)
# figure out layout such that there are more columns than rows
while n_cols < n_rowsAdj:
n_cols = n_cols + 1
n_rowsAdj = n_rows/n_cols
if n_rows % n_cols*n_rowsAdj > 0:
#n_rowsAdj = n_rowsAdj+1
n_cols = n_cols + 1
#fig = plt.figure()
for i in range(n_clusters):
iout = im.new('L',(m_frameBinned,n_frameBinned),"black")
g0 = code==i
g0 = g0.astype(np.uint8)*255
iout.putdata(list(g0))
iout = iops.colorize(iout,(0,0,0),(255,0,0))
#iout.save("cluster_0.tif")
# blend mean of stack with this cluster's regions. flip image top to bottom
ioutBlend = (im.blend(imean,iout,0.5)).transpose(im.FLIP_TOP_BOTTOM)
#ioutBlend.save("cluster_" + str(i) + ".tif")
#ax = fig.add_subplot(n_rowsAdj,n_cols,i+1,frame_on=False)
ax = plt.subplot(n_rowsAdj,n_cols,i+1)
plt.imshow(ioutBlend)
plt.xlabel(str(i+1))
plt.setp(ax.get_xticklabels(), visible=False)
plt.setp(ax.get_yticklabels(), visible=False)
plt.savefig(sz_fbase + "_clusters.pdf",dpi=300,format="pdf")
plt.clf()
# save traces out to text file
fout = open(sz_fbase + "_signals.txt",'w')
details = get_data("details.xls")
for customer_detail in details["Sheet1"]:
im=Image.open("2.png")
f = ImageFont.truetype("avantgarde.otf",14)
name_txt=Image.new('L', (500,500))
name_block = ImageDraw.Draw(name_txt)
name_block.text( (15, 38), customer_detail[0], font=f, fill=255)
w=name_txt.rotate(0, expand=3)
im.paste( ImageOps.colorize(w, (0,0,0), (255,203,4)), (242,60), w)
phone_txt = Image.new('L',(500,500))
phone_block = ImageDraw.Draw(phone_txt)
phone_block.text( (15,70), str(customer_detail[1]), font=f, fill=255)
w=phone_txt.rotate(0, expand=3)
im.paste( ImageOps.colorize(w, (0,0,0), (0,0,0)), (242,60), w)
comp_txt= Image.new('L',(500,500))
comp_block = ImageDraw.Draw(comp_txt)
comp_block.text( (30,98), customer_detail[2], font=f, fill=255)
w=comp_txt.rotate(0, expand=3)
im.paste( ImageOps.colorize(w, (0,0,0), (0,0,0)), (242,60), w)
route_txt= Image.new('L',(500,500))
route_block = ImageDraw.Draw(route_txt)
def WeatherScreenshot():
debug("\n ### WeatherScreenshot [%s] ### " % time.ctime())
debug("Threading image acquisition")
#th = threading.Thread(target=GetPhoto)
#th.start()
#twd = threading.Thread(target=TheWalkingDead, args=(th,))
#twd.walker = "Testing"
#twd.start()
#if not twd.is_alive():
# sys.exit(1)
ReadConfig()
debug("Autenticating in Twitter")
# App python-tweeter
# https://dev.twitter.com/apps/815176
tw = twitter.Api(
consumer_key = cons_key,
consumer_secret = cons_sec,
access_token_key = acc_key,
access_token_secret = acc_sec
)
#debug("Retrieving info...")
#msg = get_content()
#th.join()
#twd.join()
#if FAILCOUNTER < 0:
# print "Failed to acquire image. Quitting..."
# sys.exit(1)
#if not msg:
msg = "Just another reboot at %s" % \
time.strftime("%H:%M", time.localtime())
tw.PostUpdate(status = msg)
if False:
msg_body = "\n".join(msg[1:])
im = Image.open(filename)
# just get truetype fonts on package ttf-mscorefonts-installer
try:
f_top = ImageFont.truetype(font="Arial", size=60)
except TypeError:
# older versions hasn't font and require full path
arialpath = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf"
f_top = ImageFont.truetype(arialpath, size=60)
try:
f_body = ImageFont.truetype(font="Arial", size=20)
except TypeError:
# older versions hasn't font and require full path
arialpath = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf"
f_body = ImageFont.truetype(arialpath, size=20)
# SHADOW
step = 1
for c in [ WHITE, BLACK ]:
txt = Image.new('L', IMGSIZE)
d = ImageDraw.Draw(txt)
d.text( (10 + step, 10 + step), msg[0], font=f_top, fill=255)
position = 80
for m in msg[1:]:
d.text( (10 + step, position + step), m, font=f_body, fill=255)
position += 20
w = txt.rotate(0, expand=1)
step = 0
im.paste(ImageOps.colorize(w, c, c), (0,0), w)
im.save(filename)
# adding the credit to the right guys (awesome guys btw)
msg = u"%s \nvia http://forecast.io/#/f/59.4029,17.9436" % "\n".join(msg)
try:
print u"%s" % msg
except UnicodeEncodeError:
# I just hate this...
pass
if sys.argv[-1] == "dry-run":
debug("Just dry-run mode. Done!")
return
try:
#tw.PostMedia(status = msg,media = filename)
tw.Post(status = msg)
debug("done!")
except:
print "Failed for some reason..."
# it failed so... deal w/ it.
pass
else:
print "no message available"
def sphereToPicture(sphere):
picture = normalize(sphere)
picture = ImageOps.colorize(picture, (10, 0, 100), (0, 256, 0))
picture = imageToPygame(picture)
return picture
def draw_and_compare():
#global save_im, remaining, fail_count, last_saved_count
global colors
save_im_copy = whistler.save_im.copy()
#poly_rect_area = get_rand_rect()
rx1, ry1 = randint(0, whistler.width), randint(0, whistler.height)
rim = choice(imgs)
canvasOffset = 0
rx1 = (rx1 - ((rx1 - canvasOffset) % rim.size[0]));
ry1 = (ry1 - ((ry1 - canvasOffset) % rim.size[1]));
offset = choice([1,2,3,4,5,6])
if offset==1:
rx1 = rx1 - rim.size[0]/2
ry1 = ry1 - rim.size[1]/2
if offset==2:
rx1 = rx1 - rim.size[0]/2
ry1 = ry1 + rim.size[1]/2
if offset==3:
rx1 = rx1 + rim.size[0]/2
ry1 = ry1 - rim.size[1]/2
if offset==4:
rx1 = rx1 + rim.size[0]/2
ry1 = ry1 + rim.size[1]/2
rangle = randint(0,359)
rim = rim.rotate(rangle, Image.NEAREST, expand=True)
if choice([1,2]) == 2:
rim = rim.transpose(Image.FLIP_LEFT_RIGHT)
if choice([1,2]) == 2:
rim = rim.transpose(Image.FLIP_TOP_BOTTOM)
rx2 = rx1 + rim.size[0]
ry2 = ry1 + rim.size[1]
#save_im_crop = whistler.save_im.crop((rx1, ry1, rx2, ry2))
#save_im_crop.load()
#draw_rand_polys(save_im_crop)
im_crop = whistler.im.crop((rx1, ry1, rx2, ry2))
save_im_copy_crop = save_im_copy.crop((rx1, ry1, rx2, ry2))
im_crop.load(), save_im_copy_crop.load()
r,g,b = varyb(vary(choice(colors)))
rc, bc, bc, ralpha = rim.split()
blob = ImageOps.colorize(ImageOps.grayscale(rim.convert('RGB')),(r,g,b,0), (255,255,255,0))
#blob = rim.convert('RGB')
blob.filter(ImageFilter.BLUR)
ralpha.filter(ImageFilter.BLUR)
blob.putalpha(ralpha)
whistler.save_im.paste(blob,
(rx1, ry1), mask=ralpha)
painted_crop = whistler.save_im.crop((rx1, ry1, rx2, ry2))
painted_crop.load()
old_diff = whistler.abs_diff(save_im_copy_crop,im_crop)
new_diff = whistler.abs_diff(painted_crop,im_crop)
if new_diff < old_diff:
whistler.remaining -= old_diff-new_diff
#print ':\timproved\t' + str(old_diff-new_diff)\
# + '\tremaining:\t' + str(remaining)
whistler.last_saved_count = 0
whistler.fail_count=0
else:
whistler.save_im = save_im_copy
whistler.fail_count +=1
def triangles(original,
n=30,
size=150,
width=700,
height=700,
min_distance=70,
opacity=220):
original = original.convert('RGB')
colours = util.get_dominant_colours(original, 8)
colours_ordered = util.order_colours_by_brightness(colours)
brightest_colour = list(random.choice(colours_ordered[:3]))
brightest_colour.append(0)
new = Image.new('RGBA', (width, height), tuple(brightest_colour))
draw = aggdraw.Draw(new)
centres = []
def is_too_close(x, y):
for centre in centres:
if math.sqrt(
math.pow(centre[0] - x, 2) +
math.pow(centre[1] - y, 2)) < min_distance:
return True
return False
for i in xrange(n):
colour = tuple(colours[int(random.randint(0, len(colours) - 1))])
x = random.randint(size / 2, width - 1 - size / 2)
y = random.randint(size / 2, height - 1 - size / 2)
if is_too_close(x, y):
continue
centres.append((x, y))
brush = aggdraw.Brush(colour, opacity)
points = get_triangle_path(x, y, size / 2, size / 2)
draw.polygon(points, None, brush)
draw.flush()
brightest_colour = brightest_colour[0:3]
texture = Image.open(
os.path.dirname(os.path.abspath(__file__)) + '/' +
'assets/airbrush.png')
texture = texture.convert('RGBA')
r, g, b, a = texture.split()
texture = ImageOps.grayscale(texture)
texture = ImageOps.colorize(texture, (0, 0, 0), tuple(brightest_colour))
texture = texture.convert('RGBA')
texture.putalpha(a)
r, g, b, a = new.split()
texture = texture.crop((0, 0, width, height))
texture_layer = Image.new('RGBA', (width, height), (0, 0, 0, 0))
texture_layer.paste(texture, mask=new)
new.paste(texture_layer, mask=texture_layer)
im = Image.new('RGB', (width, height), tuple(brightest_colour))
im.paste(new, mask=a)
return im
dt = t[int(i*len(t)/O)] - t0
t0 = t[int(i*len(t)/O)]
#current star color
color = cols[int(i*len(t)/O)]
#take next gif image
image = im[i % N]
#get image size
isize = image.size
bsize = tuple((isize[0]*2,isize[1]))
size = tuple([int(z * R[int(i*len(t)/O)]) for z in isize])
#apply color transform to image
image.load()
r, g, b, alpha = image.split()
gray = ImageOps.grayscale(image)
img = ImageOps.colorize(gray, (0,0,0,0), color)
img.putalpha(alpha)
#resize transform to image
img = img.resize(size)
#apply filter to image
#omage = omage.filter(ImageFilter.SMOOTH_MORE)
#generate HR plot
sub.plot(np.log10(Teff)[:int(i*len(t)/O)+1], logL[:int(i*len(t)/O)+1], 'b.', ms=4)
sub.title.set_color('white')
sub.yaxis.label.set_color('white')
sub.xaxis.label.set_color('white')
sub.tick_params(axis='x', colors='white')
sub.tick_params(axis='y', colors='white')
def plot_ld_heatmap(mat_file,
bin_file,
outfile,
window_size=500000,
summary_stat="unlinked_pct",
cmap=DEFAULT_CMAP,
missing_color=(255, 255, 255),
bg_color=(255, 255, 255),
chrm_color=(0, 0, 0),
tics=False,
font_file="/Library/Fonts/Microsoft/Arial.ttf",
font_size=80):
"""
Create a triangle heatmap plot from a numpy matrix of pairwise-bin values. Each cel of the
matrix is a summary statistic (e.g. mean or 95th percentile) of the LD between the two bins.
The matrix can either be square or upper-right-hand. bins is a three-column matrix:
chrmosome, start position, summary value.
TODO: support creating diamond heatmaps from a square matrix.
"""
import csv
def load_matrix(x, first):
with open(abspath(x), "rU") as i:
r = csv.reader(i, delimiter=",")
h = r.next()[first:]
m = np.array(list(
map(lambda x: float("nan" if x == "NA" else x), row[first:])
for row in r),
dtype=np.float64)
return (h, m)
mat = load_matrix(mat_file, 1)[1]
#mat = mat[0:5063,0:5063]
bin_cols, bins = load_matrix(bin_file, 0)
#bins = bins[0:5063,]
chrm_col = which("chrm", bin_cols)
stat_col = which(summary_stat, bin_cols)
chrms = bins[:, chrm_col]
chrm_idxs = np.unique(chrms, return_index=True)[1]
chrms = [int(chrms[index]) for index in sorted(chrm_idxs)]
# TODO: this is a hack. Fix the process_ld_file function to write blank lines for missing windows
row = 0
nan = float("nan")
blank = [nan] * (bins.shape[1] - 3)
for chrm in chrms:
pos = 0
while row < bins.shape[0] and int(bins[row, chrm_col]) == chrm:
if int(bins[row, 1]) != pos:
bins = np.insert(bins, row, [chrm, pos, 0] + blank, axis=0)
mat = np.insert(mat, row, nan, axis=0)
mat = np.insert(mat, row, nan, axis=1)
row += 1
pos += window_size
mat_size = mat.shape[0]
assert mat_size == mat.shape[1], "Matrix is not square"
assert mat_size == len(bins), "Matrix and bins are of different size"
def convert_chrm(c):
c = int(c)
return "X" if c == 23 else str(c)
chrms = map(convert_chrm, bins[..., chrm_col])
im = Image.new("RGB", (mat_size + X_OFFSETS[4], mat_size + Y_OFFSETS[0]),
bg_color)
pixels = im.load()
draw = ImageDraw.Draw(im)
font = ImageFont.truetype(font_file, font_size)
chrm_id = None
chrm_end = 0
tic_interval = 10000000 / window_size
for row, summary in enumerate(bins[..., stat_col]):
chrm = chrms[row]
def get_line_coords(start, end):
x1 = row + X_OFFSETS[start]
y1 = row + Y_OFFSETS[start]
x2 = row + X_OFFSETS[end]
y2 = row + Y_OFFSETS[end]
return ((x1, y1), (x2, y2))
# draw summary line
color = heatmap(summary,
cmap) if not np.isnan(summary) and summary > 0 else 0
draw.line(get_line_coords(2, 3), fill=color)
for col in xrange(row, mat_size):
x = col + X_OFFSETS[4]
val = mat[row, col]
if np.isnan(val) or val < 0:
pixels[x, row] = missing_color
else:
pixels[x, row] = heatmap(val, cmap)
# Label chromosome boundaries
if chrm != chrm_id or row == (mat_size - 1):
draw.line(get_line_coords(0, 2), fill=chrm_color, width=5)
if chrm_id is not None:
# first draw text in a blank image, then rotate and paste into the main image
txt = str(chrm_id)
txt_size = draw.textsize(txt, font=font)
txt_img = Image.new("L", txt_size)
txt_draw = ImageDraw.Draw(txt_img)
txt_draw.text((0, 0), txt, font=font, fill=255)
txt_img = txt_img.rotate(-45, expand=1)
offset = max(txt_size[0], txt_size[1])
lft_indent = int(math.floor((txt_img.size[0] - offset) / 2))
top_indent = int(math.floor((txt_img.size[1] - offset) / 2))
txt_img = txt_img.crop(
(lft_indent, top_indent, txt_img.size[0] - lft_indent,
txt_img.size[1] - top_indent))
text_row = int(chrm_end + ((row - chrm_end) / 2))
text_x = int(text_row + X_OFFSETS[0] +
((X_OFFSETS[2] - X_OFFSETS[0]) / 2) -
(txt_img.size[0] / 2))
text_y = int(text_row + Y_OFFSETS[0] +
((Y_OFFSETS[2] - Y_OFFSETS[0]) / 2) -
(txt_img.size[1] / 2))
im.paste(ImageOps.colorize(txt_img, bg_color, chrm_color),
(text_x, text_y))
chrm_id = chrm
chrm_end = row
# add tics
if tics and ((row - chrm_end) % tic_interval) == 0:
draw.line(get_line_coords(1, 2), fill=chrm_color, width=3)
# convert to RGBA (required for background recoloring)
im2 = im.convert("RGBA")
# rotate
im2 = im2.rotate(45, expand=True)
# recolor background
bg = Image.new("RGBA", im2.size, (255, ) * 4)
im2 = Image.composite(im2, bg, im2)
# convert back to RGB
im = im2.convert(im.mode)
# crop
final_height = int(math.ceil(
math.sqrt(2 * math.pow(mat_size, 2)) / 2)) + OFFSETS[-1]
im = im.crop((0, 0, im.size[0], final_height))
# save
im.save(outfile)
def add_text_image(self, text_image, offset = (242,60)):
self.base.paste(ImageOps.colorize(text_image, (0,0,0), self.colour), offset, text_image)
return self.base
def counting(c_std, a_std, imageFile):
image_list = [imageFile]
c_std = float(c_std)
if image_list[0][-3:] == "tif":
for f, filename in enumerate(image_list):
subprocess.call(["convert", filename, filename + ".png"])
image_list[f] = filename + ".png"
output_filename_hash = datetime.datetime.now().minute * 60 + datetime.datetime.now().second
images = [scipy.misc.imread(filename).astype(np.uint16) for filename in image_list]
# correlation_matrix = np.array([[-1, -1, -1, -1, -1],
# [-1, -1, -1, -1, -1],
# [-1, -1, 24, -1, -1],
# [-1, -1, -1, -1, -1],
# [-1, -1, -1, -1, -1]])
correlation_matrix = np.array(
[
[-5935, -5935, -5935, -5935, -5935],
[-5935, 8027, 8027, 8027, -5935],
[-5935, 8027, 30742, 8027, -5935],
[-5935, 8027, 8027, 8027, -5935],
[-5935, -5935, -5935, -5935, -5935],
]
)
median_diameter = 5
local_max = 3
# c_std = 1
processed_images = [np.copy(image).astype(np.int64) for image in images]
processed_images = [
np.subtract(image, np.minimum(spf.median_filter(image, median_diameter), image)) for image in images
]
processed_images = [
np.maximum(scipy.signal.correlate(image, correlation_matrix, mode="same"), np.zeros_like(image)).astype(
np.int64
)
for image in processed_images
]
thresholded_images = [
image > np.mean(image) + c_std * np.std(image)
# images[i] > np.mean(images[i]) + a_std * np.std(images[i])
# images[i] > a_std
for i, image in enumerate(processed_images)
]
for i, mask in enumerate(thresholded_images):
for (h, w), valid in np.ndenumerate(mask):
if valid:
local_slice = np.copy(
processed_images[i][h - local_max : h + local_max + 1, w - local_max : w + local_max + 1]
)
if (
h + local_max >= mask.shape[0]
or w + local_max >= mask.shape[1]
or h - local_max < 0
or w - local_max < 0
):
mask[h, w] = False
continue
local_slice[local_max, local_max] = 0
if np.amax(local_slice) >= processed_images[i][h, w]:
mask[h, w] = False
size = 4
for i, image in enumerate(images):
i_std = np.std(image)
i_median = np.median(image) - i_std
i_max = np.amax(image)
for (h, w), value in np.ndenumerate(image):
if image[h, w] > i_median:
image[h, w] = int(
np.around(math.sqrt(image[h, w] - i_median) / math.sqrt(i_max - i_median) * float(2 ** 8 - 1))
)
else:
image[h, w] = 0
output_images = [
ImageOps.colorize(Image.fromstring("L", image.shape, image.astype(np.uint8)), (0, 0, 0), (255, 255, 255))
for image in images
]
for i, image in enumerate(images):
for (h, w), value in np.ndenumerate(image):
if thresholded_images[i][h, w]:
box = ((w - size, h - size), (w + size, h + size))
draw = ImageDraw.Draw(output_images[i])
draw.rectangle(box, fill=None, outline="blue")
# Editing the output file name; Will have the same as the filename + png
[
image.save(
str(i).zfill(int(np.ceil(math.log(len(output_images), 10))))
+ " SIMPLE "
+ str(output_filename_hash)
+ ".png"
)
for i, image in enumerate(output_images)
]
for i, image in enumerate(thresholded_images):
print(str(i).zfill(int(np.ceil(math.log(len(thresholded_images), 10)))) + " " + str(np.sum(np.sum(image))))
def cf_image(cfs,
coords,
width=None,
height=None,
pos=(0, 0),
size=26,
border=5,
bg=(0, 0, 0),
colmap=None):
"""
Returns a PIL image showing the selected connection fields (CFS)
as supplied by extract_CFs. Does not support non-square CF
shapes.
'cfs' is an ndarray of N dstacked cfs, each of shape (X,X): (X,X,N)
'coords' is an ndarray of N coordinates: (N,2)
'width' and 'height' are either None (full) of integer grid sizes
'pos' is the starting position of the block, (x,y)
'size' and 'border' are the cf image size and the border size in pixels.
'colmap' is an RGB array shape (N,M,3) with values between 0.0 and 1.0.
"""
normalize = lambda arr: (arr - arr.min()) / (arr.max() - arr.min())
cf_im = lambda cf, size: greyscale(normalize(cf)).resize(
(size, size), Image.NEAREST)
(posx, posy) = pos
(d1, d2) = zip(*coords)
density = len(set(d1))
assert density == len(set(d2)), "Not implemented for non-square sets"
height = density if height is None else height
width = density if width is None else width
assert height > 0 and width > 0, "Height and width must be None or greater than zero"
assert posx + width <= density, "X position and width greater than density"
assert posy + height <= density, "Y position and width greater than density"
# Functions mapping original coordinates onto consecutive grid indices
fst_map = dict(((ind, i) for (i, ind) in enumerate(sorted(set(d1)))))
snd_map = dict(((ind, i) for (i, ind) in enumerate(sorted(set(d2)))))
# Generating a dictionary from the grid coordinates to the CF index
mapped_coords = [(fst_map[fst], snd_map[snd]) for [fst, snd] in coords]
indexed_coords = dict(
(coord, i) for (i, coord) in enumerate(mapped_coords))
# Initialising the image
imwidth = width * size + (width - 1) * border
imheight = height * size + (height - 1) * border
cf_block = Image.new('RGB', (imwidth, imheight), bg)
# Building image row by row, top to bottom.
for yind in range(height):
for xind in range(width):
# Swapped coordinate system
cf_ind = indexed_coords[(yind + posy, xind + posx)]
# Get color from the color map if available
if colmap is not None:
crd1, crd2 = coords[cf_ind]
r, g, b = colmap[crd1, crd2, :]
color = (r * 255, g * 255, b * 255)
else:
color = (255, 255, 255)
cf = cfs[:, :, cf_ind]
(cf_dim1, cf_dim2) = cf.shape
assert cf_dim1 == cf_dim2, "Only supports square CFs."
cf_image = ImageOps.colorize(cf_im(cf, size), (0, 0, 0, 0), color)
xoffset = xind * border
yoffset = yind * border
paste_coord = (xoffset + xind * size, yoffset + yind * size)
cf_block.paste(cf_image, paste_coord)
return cf_block
dpf = ImageFont.truetype ("datapro.ttf", fs)
def getrow(i):
return 5 + ulpaste[1] + im.size[1] - slotwidth * (i + 1)
for i in xrange(slots):
draw.text ((ulpaste[0] - 6 * slotwidth, getrow(i) ),
"0x%08x" % (i * 0x02000000), fill="#444444", font=dpf)
for row in xrange(32):
txt=Image.new("L", (600,60))
d = ImageDraw.Draw(txt)
d.text ((0,0), "0x%08x" % (row * 0x00100000), fill=255, font=dpf)
del d
rtxt = txt.rotate (17.5, expand=1)
fim.paste (ImageOps.colorize(rtxt, "#ffffff", "#444444"),
(ulpaste[0] + (row*(p_per_col/32)*pheight), ulpaste[1] - 4*slotwidth), rtxt)
del txt
del rtxt
#draw.text ((ulpaste[0] + 0x00011000 * p_per_col*pheight / (32*1024*1024), ulpaste[1] + 65*slotwidth),
# "Code/Data", fill="#000000", font=dpf)
#draw.text ((ulpaste[0] + 0x018C0000 * p_per_col*pheight / (32*1024*1024), ulpaste[1] + 65*slotwidth),
# "Stack/Heap", fill="#000000", font=dpf)
def writerow(i, str):
draw.text ((10 * slotwidth, getrow(i) ), str, fill="#000000", font=dpf)
writerow (0, "Slot 0: Active Process")
writerow (1, "Slot 1: ROM Image")
def makecolourediconset(shape, icon_colours, bg):
coloured_images = []
for col in icon_colours:
coloured_images.append(ImageOps.colorize(shape, col, bg))
coloured_images.append(ImageOps.colorize(shape, bg, bg))
return coloured_images
def plot_ld_heatmap(mat_file, bin_file, outfile, window_size=500000, summary_stat="unlinked_pct",
cmap=DEFAULT_CMAP, missing_color=(255, 255, 255), bg_color=(255, 255, 255), chrm_color=(0, 0, 0),
tics=False, font_file="/Library/Fonts/Microsoft/Arial.ttf", font_size=80):
"""
Create a triangle heatmap plot from a numpy matrix of pairwise-bin values. Each cel of the
matrix is a summary statistic (e.g. mean or 95th percentile) of the LD between the two bins.
The matrix can either be square or upper-right-hand. bins is a three-column matrix:
chrmosome, start position, summary value.
TODO: support creating diamond heatmaps from a square matrix.
"""
import csv
def load_matrix(x, first):
with open(abspath(x), "rU") as i:
r = csv.reader(i, delimiter=",")
h = r.next()[first:]
m = np.array(list(map(lambda x: float("nan" if x == "NA" else x), row[first:]) for row in r), dtype=np.float64)
return (h, m)
mat = load_matrix(mat_file, 1)[1]
#mat = mat[0:5063,0:5063]
bin_cols, bins = load_matrix(bin_file, 0)
#bins = bins[0:5063,]
chrm_col = which("chrm", bin_cols)
stat_col = which(summary_stat, bin_cols)
chrms = bins[:,chrm_col]
chrm_idxs = np.unique(chrms, return_index=True)[1]
chrms = [int(chrms[index]) for index in sorted(chrm_idxs)]
# TODO: this is a hack. Fix the process_ld_file function to write blank lines for missing windows
row = 0
nan = float("nan")
blank = [nan] * (bins.shape[1]-3)
for chrm in chrms:
pos = 0
while row < bins.shape[0] and int(bins[row, chrm_col]) == chrm:
if int(bins[row, 1]) != pos:
bins = np.insert(bins, row, [chrm, pos, 0] + blank, axis=0)
mat = np.insert(mat, row, nan, axis=0)
mat = np.insert(mat, row, nan, axis=1)
row += 1
pos += window_size
mat_size = mat.shape[0]
assert mat_size == mat.shape[1], "Matrix is not square"
assert mat_size == len(bins), "Matrix and bins are of different size"
def convert_chrm(c):
c = int(c)
return "X" if c == 23 else str(c)
chrms = map(convert_chrm, bins[...,chrm_col])
im = Image.new("RGB", (mat_size + X_OFFSETS[4], mat_size + Y_OFFSETS[0]), bg_color)
pixels = im.load()
draw = ImageDraw.Draw(im)
font = ImageFont.truetype(font_file, font_size)
chrm_id = None
chrm_end = 0
tic_interval = 10000000 / window_size
for row, summary in enumerate(bins[...,stat_col]):
chrm = chrms[row]
def get_line_coords(start, end):
x1 = row + X_OFFSETS[start]
y1 = row + Y_OFFSETS[start]
x2 = row + X_OFFSETS[end]
y2 = row + Y_OFFSETS[end]
return ((x1, y1), (x2, y2))
# draw summary line
color = heatmap(summary, cmap) if not np.isnan(summary) and summary > 0 else 0
draw.line(get_line_coords(2, 3), fill=color)
for col in xrange(row, mat_size):
x = col + X_OFFSETS[4]
val = mat[row,col]
if np.isnan(val) or val < 0:
pixels[x, row] = missing_color
else:
pixels[x, row] = heatmap(val, cmap)
# Label chromosome boundaries
if chrm != chrm_id or row == (mat_size - 1):
draw.line(get_line_coords(0, 2), fill=chrm_color, width=5)
if chrm_id is not None:
# first draw text in a blank image, then rotate and paste into the main image
txt = str(chrm_id)
txt_size = draw.textsize(txt, font=font)
txt_img = Image.new("L", txt_size)
txt_draw = ImageDraw.Draw(txt_img)
txt_draw.text((0, 0), txt, font=font, fill=255)
txt_img = txt_img.rotate(-45, expand=1)
offset = max(txt_size[0], txt_size[1])
lft_indent = int(math.floor((txt_img.size[0] - offset) / 2))
top_indent = int(math.floor((txt_img.size[1] - offset) / 2))
txt_img = txt_img.crop((lft_indent, top_indent,
txt_img.size[0] - lft_indent, txt_img.size[1] - top_indent))
text_row = int(chrm_end + ((row - chrm_end) / 2))
text_x = int(text_row + X_OFFSETS[0] + ((X_OFFSETS[2] - X_OFFSETS[0]) / 2) - (txt_img.size[0] / 2))
text_y = int(text_row + Y_OFFSETS[0] + ((Y_OFFSETS[2] - Y_OFFSETS[0]) / 2) - (txt_img.size[1] / 2))
im.paste(ImageOps.colorize(txt_img, bg_color, chrm_color), (text_x, text_y))
chrm_id = chrm
chrm_end = row
# add tics
if tics and ((row - chrm_end) % tic_interval) == 0:
draw.line(get_line_coords(1, 2), fill=chrm_color, width=3)
# convert to RGBA (required for background recoloring)
im2 = im.convert("RGBA")
# rotate
im2 = im2.rotate(45, expand=True)
# recolor background
bg = Image.new("RGBA", im2.size, (255,)*4)
im2 = Image.composite(im2, bg, im2)
# convert back to RGB
im = im2.convert(im.mode)
# crop
final_height = int(math.ceil(math.sqrt(2 * math.pow(mat_size, 2)) / 2)) + OFFSETS[-1]
im = im.crop((0, 0, im.size[0], final_height))
# save
im.save(outfile)
def sphereToPicture(sphere):
picture = normalize(sphere)
picture = ImageOps.colorize(picture, (10,0,100), (0,256,0))
picture = imageToPygame(picture)
return picture
def WeatherScreenshot():
global filename
debug("\n ### WeatherScreenshot [%s] ### " % time.ctime())
debug("Threading image acquisition")
th = threading.Thread(target=GetPhoto)
th.start()
twd = threading.Thread(target=TheWalkingDead, args=(th, ))
twd.walker = "Testing"
twd.start()
if not twd.is_alive():
sys.exit(1)
ReadConfig()
debug("Autenticating in Twitter")
# App python-tweeter
# https://dev.twitter.com/apps/815176
tw = twitter.Api(consumer_key=cons_key,
consumer_secret=cons_sec,
access_token_key=acc_key,
access_token_secret=acc_sec)
debug("Retrieving info...")
msg = get_content()
th.join()
twd.join()
if FAILCOUNTER < 0:
print("Failed to acquire image. Quitting...")
sys.exit(1)
if not msg:
msg = "Just another shot at %s" % \
time.strftime("%H:%M", time.localtime())
if msg:
im = Image.open(filename)
# just get truetype fonts on package ttf-mscorefonts-installer
try:
f_top = ImageFont.truetype(font="Impact", size=60)
except TypeError:
# older versions hasn't font and require full path
arialpath = "/usr/share/fonts/truetype/msttcorefonts/Impact.ttf"
f_top = ImageFont.truetype(arialpath, size=60)
try:
f_body = ImageFont.truetype(font="Arial", size=20)
except TypeError:
# older versions hasn't font and require full path
arialpath = "/usr/share/fonts/truetype/msttcorefonts/Arial.ttf"
f_body = ImageFont.truetype(arialpath, size=20)
"""
# SHADOW
step = 1
for c in [ WHITE, BLACK ]:
txt = Image.new('L', IMGSIZE)
d = ImageDraw.Draw(txt)
d.text( (10 + step, 10 + step), msg[0], font=f_top, fill=255)
position = 80
for m in msg[1:]:
d.text( (10 + step, position + step), m, font=f_body, fill=255)
position += 20
w = txt.rotate(0, expand=1)
step = 0
im.paste(ImageOps.colorize(w, c, c), (0,0), w)
im.save(filename)
"""
step = 0
debug("Writting in WHITE")
txt = Image.new('L', IMGSIZE)
d = ImageDraw.Draw(txt)
## Title ##
# border first
d.text((10 + step + 1, 10 + step), msg[0], font=f_top, fill=255)
d.text((10 + step - 1, 10 + step), msg[0], font=f_top, fill=255)
d.text((10 + step, 10 + step + 1), msg[0], font=f_top, fill=255)
d.text((10 + step, 10 + step - 1), msg[0], font=f_top, fill=255)
## Body ##
position = 80
for m in msg[1:]:
# border first
d.text((10 + step + 1, position + step), m, font=f_body, fill=255)
d.text((10 + step - 1, position + step), m, font=f_body, fill=255)
d.text((10 + step, position + step + 1), m, font=f_body, fill=255)
d.text((10 + step, position + step - 1), m, font=f_body, fill=255)
# content
d.text((10 + step, position + step), m, font=f_body, fill=255)
position += 20
# final touch
w = txt.rotate(0, expand=1)
im.paste(ImageOps.colorize(w, WHITE, WHITE), (0, 0), w)
im.save(filename)
debug("Writting in BLACK")
txt = Image.new('L', IMGSIZE)
d = ImageDraw.Draw(txt)
# content
d.text((10 + step, 10 + step), msg[0], font=f_top, fill=255)
position = 80
for m in msg[1:]:
# content
d.text((10 + step, position + step), m, font=f_body, fill=255)
position += 20
# final touch
w = txt.rotate(0, expand=1)
im.paste(ImageOps.colorize(w, BLACK, BLACK), (0, 0), w)
im.save(filename)
# adding the credit to the right guys (awesome guys btw)
msg = u"%s \nvia http://forecast.io/#/f/59.4029,17.9436" % "\n".join(
msg)
try:
print(u"%s" % msg)
except UnicodeEncodeError:
# I just hate this...
pass
if sys.argv[-1] == "dry-run":
debug("Just dry-run mode. Done!")
return
try:
tw.PostUpdate(status=msg, media=filename)
debug("done!")
except Exception as e:
print("Failed for some reason:", e)
# it failed so... deal w/ it.
pass
else:
print("no message available")