def load_raw_slide_to_cache(slide_id, resource):
# Get the data for this slide
sr = get_slide_ref(slide_id)
if sr is not None:
sr.get_local_copy(resource)
else:
print('Slide %s not found' % (slide_id, ))
def api_get_slide_random_patch(task_id, slide_id, width):
db = get_db()
# Find out which machine the slide is currently being served from
# Get the tiff image from which to sample the region of interest
sr = get_slide_ref(slide_id)
# Get the identifiers for the slide
# TODO: what to do with project here?
(project, specimen, block, slide_name, slide_ext) = sr.get_id_tuple()
# Are we de this slide to a different node?
del_url = find_delegate_for_slide(slide_id)
# If local, call the method directly
rawbytes = None
if del_url is None:
rawbytes = get_random_patch(project, specimen, block, 'raw',
slide_name, slide_ext, 0, width,
'png').data
else:
url = '%s/dzi/random_patch/%s/%s/%s/raw/%s.%s/%d/%d.png' % (
del_url, project, specimen, block, slide_name, slide_ext, 0, width)
pr = sr.get_project_ref()
post_data = urllib.urlencode(
{'project_data': json.dumps(pr.get_dict())})
rawbytes = urllib2.urlopen(url, post_data).read()
# Send the patch
resp = make_response(rawbytes)
resp.mimetype = 'image/png'
return resp
def export_annot_vtk(task, slide_id, out_file):
""" Export annotations on a slide to VTK file """
# Find the annotation in the database
db = get_db()
rc = db.execute('SELECT json FROM annot WHERE slide_id=? AND task_id=?',
(slide_id, task)).fetchone()
if rc is not None:
# Get the annotation
data = json.loads(rc['json'])
# Get the raw slide dimensions
sr = get_slide_ref(slide_id)
dims = get_slide_raw_dims(sr)
if dims is None:
sys.exit("Missing slide dimensions information")
# Get the set of points
pts = annot_sample_path_curves(data, 5000)
# Join all the point arrays
all_pts = [item for sublist in pts for item in sublist]
# Length of each polyline segment
plen = [len(sublist) for sublist in pts]
# Write a VTK file based on points
out_file.write("# vtk DataFile Version 4.2\n")
out_file.write("vtk output\n")
out_file.write("ASCII\n")
out_file.write("DATASET POLYDATA\n")
out_file.write("POINTS %d float\n" % len(all_pts))
# Write all the points
for p in all_pts:
out_file.write('%f %f %f\n' % (p[0], p[1], 0.0))
out_file.write("LINES %d %d\n" % (len(pts), len(pts) + sum(plen)))
idx = 0
for q in pts:
out_file.write(
'%d %s\n' %
(len(q), ' '.join([str(x) for x in range(idx, idx + len(q))])))
idx = idx + len(q)
def api_slide_job_status(task_id, slide_id, jobid):
db = get_db()
sr = get_slide_ref(slide_id)
(project, specimen, block, slide_name, slide_ext) = sr.get_id_tuple()
# Are we de this slide to a different node?
del_url = find_delegate_for_slide(slide_id)
# If local, call the method directly
if del_url is None:
return dzi_job_status(project, slide_name, jobid)
else:
url = '%s/dzi/job/%s/%s/%s/status' % (
del_url, project, slide_name, jobid)
pr = sr.get_project_ref()
post_data = urllib.urlencode({'project_data': json.dumps(pr.get_dict())})
return urllib2.urlopen(url, post_data).read()
def generate_sample_patch(slide_id, sample_id, rect, dims=(512, 512), level=0):
# Find out which machine the slide is currently being served from
# Get the tiff image from which to sample the region of interest
db = get_db()
sr = get_slide_ref(slide_id)
# Get the identifiers for the slide
# TODO: what to do with project here?
(project, specimen, block, slide_name, slide_ext) = sr.get_id_tuple()
# Are we de this slide to a different node?
del_url = find_delegate_for_slide(slide_id)
# Compute the parameters
ctr_x = int((rect[0] + rect[2]) / 2.0 + 0.5)
ctr_y = int((rect[1] + rect[3]) / 2.0 + 0.5)
(w, h) = dims
x = ctr_x - ((w - int(w / 2.0)) - 1)
y = ctr_y - ((h - int(h / 2.0)) - 1)
# If local, call the method directly
rawbytes = None
if del_url is None:
rawbytes = get_patch(project, specimen, block, 'raw', slide_name,
slide_ext, level, ctr_x, ctr_y, w, h, 'png').data
else:
url = '%s/dzi/patch/%s/%s/%s/raw/%s.%s/%d/%d_%d_%d_%d.png' % (
del_url, project, specimen, block, slide_name, slide_ext, level,
ctr_x, ctr_y, w, h)
pr = sr.get_project_ref()
post_data = urllib.urlencode(
{'project_data': json.dumps(pr.get_dict())})
rawbytes = urllib2.urlopen(url, post_data).read()
# Save as PNG
with open(get_sample_patch_filename(sample_id), 'wb') as f:
f.write(rawbytes)
# Record that patch has been written
db.execute('UPDATE training_sample SET have_patch=1 where id=?',
(sample_id, ))
db.commit()
def update_slide_derived_data(slide_id, check_hash=True):
# Get the slide reference
sr = get_slide_ref(slide_id)
# Get the remote thumbnail file
f_thumb = sr.get_local_copy("thumb", check_hash=check_hash)
# Get the local thumbnail
thumb_dir = os.path.join(current_app.instance_path, 'thumb')
thumb_fn = os.path.join(thumb_dir, "thumb%08d.png" % (slide_id, ))
# If the thumb has been downloaded successfully, derive a HTML-usable thumb
if f_thumb is not None:
x = Image.open(f_thumb)
m = max(x.size[0] / 256., x.size[1] / 192.)
x = x.resize(map(int, (x.size[0] / m, x.size[1] / m)))
if not os.path.exists(thumb_dir):
os.makedirs(thumb_dir)
x.save(thumb_fn)
def get_sample_custom_png(id, level, w, h):
# Get the slide reference
db = get_db()
sample = db.execute('SELECT * FROM training_sample WHERE id=?',
(id, )).fetchone()
slide_id = sample['slide']
sr = get_slide_ref(slide_id)
# Get the identifiers for the slide
# TODO: what to do with project name here
(project, specimen, block, slide_name, slide_ext) = sr.get_id_tuple()
# Are we delegating this slide to a different node?
del_url = find_delegate_for_slide(slide_id)
# Compute the parameters
ctr_x = int((sample['x0'] + sample['x1']) / 2.0 + 0.5)
ctr_y = int((sample['y0'] + sample['y1']) / 2.0 + 0.5)
x = ctr_x - ((w - int(w / 2.0)) - 1)
y = ctr_y - ((h - int(h / 2.0)) - 1)
# If local, call the method directly
rawbytes = None
if del_url is None:
rawbytes = get_patch(project, specimen, block, 'raw', slide_name,
slide_ext, level, ctr_x, ctr_y, w, h, 'png').data
else:
url = '%s/dzi/patch/%s/%s/%s/raw/%s.%s/%d/%d_%d_%d_%d.png' % (
del_url, project, specimen, block, slide_name, slide_ext, level,
ctr_x, ctr_y, w, h)
pr = sr.get_project_ref()
post_data = urllib.urlencode(
{'project_data': json.dumps(pr.get_dict())})
rawbytes = urllib2.urlopen(url, post_data).read()
resp = make_response(rawbytes)
resp.mimetype = 'image/%s' % format
return resp
def get_affine_matrix_by_slideid(slide_id, mode, resolution='raw'):
sr = get_slide_ref(slide_id)
return get_affine_matrix(sr, mode, resolution)
def extract_svg(task, slide_id, stroke_width, strip_width, font_size,
font_color):
# The return value
svg = None
# Find the annotation in the database
db = get_db()
rc = db.execute('SELECT json FROM annot WHERE slide_id=? AND task_id=?',
(slide_id, task)).fetchone()
if rc is not None:
# Get the annotation
data = json.loads(rc['json'])
# Get the raw slide dimensions
sr = get_slide_ref(slide_id)
dims = get_slide_raw_dims(sr)
if dims is None:
raise ValueError("Missing slide dimensions information")
# Start writing svg
svg = svgwrite.Drawing(size=(dims[0], dims[1]))
# Write the paths
if 'children' in data[0][1]:
for x in data[0][1]['children']:
# Handle paths
if not check_annot_child(x):
print('Bad element:', x)
continue
try:
if x[0] == 'Path':
seg = x[1]['segments']
if len(seg) < 1 or seg[0][0][0] is None or seg[0][0][
1] is None:
continue
# Default mode is to draw curves
if strip_width is None or strip_width == 0:
# List of commands for SVG path
cmd = []
# Record the initial positioning
cmd.append('M%f,%f' % (seg[0][0][0], seg[0][0][1]))
# Record the control points
for i in range(1, len(seg)):
# Get the handles from the control point
P1 = seg[i - 1][0]
P2 = seg[i][0]
D = [P2[0] - P1[0], P2[1] - P1[1]]
V1 = seg[i - 1][2]
V2 = seg[i][1]
cmd.append('c%f,%f %f,%f %f,%f' %
(V1[0], V1[1], D[0] + V2[0],
D[1] + V2[1], D[0], D[1]))
# Add the path to the SVG
svg.add(
svg.path(d=''.join(cmd),
stroke="#000",
fill="none",
stroke_width=stroke_width))
# Alternative mode is to draw parallel strips
else:
# Record the control points
for i in range(1, len(seg)):
# Get the handles from the control point
P1 = seg[i - 1][0]
P2 = seg[i][0]
D = [P2[0] - P1[0], P2[1] - P1[1]]
V1 = seg[i - 1][2]
V2 = seg[i][1]
# Get the tangent vectors
nV1 = math.sqrt(V1[0] * V1[0] + V1[1] * V1[1])
nV2 = math.sqrt(V2[0] * V2[0] + V2[1] * V2[1])
T1 = [x / nV1 for x in V1] if nV1 > 0 else V1
T2 = [x / nV2 for x in V2] if nV2 > 0 else V2
Q2 = [
P2[0] + strip_width * T2[1],
P2[1] - strip_width * T2[0]
]
Q1 = [
P1[0] - strip_width * T1[1],
P1[1] + strip_width * T1[0]
]
DQ = [Q1[0] - Q2[0], Q1[1] - Q2[1]]
R2 = [
P2[0] - strip_width * T2[1],
P2[1] + strip_width * T2[0]
]
R1 = [
P1[0] + strip_width * T1[1],
P1[1] - strip_width * T1[0]
]
DR = [R1[0] - R2[0], R1[1] - R2[1]]
# Draw the path (part curve, part line)
svg.add(
svg.path(
d="M%f,%f c%f,%f %f,%f %f,%f L%f,%f c%f,%f %f,%f, %f,%f L%f,%f"
% (P1[0], P1[1], V1[0], V1[1],
D[0] + V2[0], D[1] + V2[1], D[0],
D[1], Q2[0], Q2[1], V2[0], V2[1],
DQ[0] + V1[0], DQ[1] + V1[1], DQ[0],
DQ[1], P1[0], P1[1]),
stroke="none",
fill="#ddd",
stroke_width=0))
# Draw the path (part curve, part line)
svg.add(
svg.path(
d="M%f,%f c%f,%f %f,%f %f,%f L%f,%f c%f,%f %f,%f, %f,%f L%f,%f"
% (P1[0], P1[1], V1[0], V1[1],
D[0] + V2[0], D[1] + V2[1], D[0],
D[1], R2[0], R2[1], V2[0], V2[1],
DR[0] + V1[0], DR[1] + V1[1], DR[0],
DR[1], P1[0], P1[1]),
stroke="none",
fill="#aaa",
stroke_width=0))
#svg.add(svg.path(
# d="M%f,%f c%f,%f %f,%f %f,%f L%f,%f L%f,%f L%f,%f" % (
# P1[0],P1[1],
# V1[0],V1[1],D[0]+V2[0],D[1]+V2[1],D[0],D[1],
# P2[0]+strip_width*T2[1],P2[1]-strip_width*T2[0],
# P1[0]-strip_width*T1[1],P1[1]+strip_width*T1[0],
# P1[0],P1[1]), stroke="#000", fill="#ddd", stroke_width=48))
elif x[0] == 'PointText':
tpos = x[1]['matrix'][4:6]
text = x[1]['content']
svg.add(
svg.text(text,
insert=tpos,
fill=font_color,
stroke=font_color,
font_size=font_size))
# ["PointText",
# {"applyMatrix": false, "matrix": [1, 0, 0, 1, 1416.62777, 2090.96831], "content": "CA2",
# "fontWeight": "bold", "fontSize": 44, "leading": 52.8, "justification": "center"}]
except TypeError:
raise ValueError("Unreadable path %s in slide %d task %d" %
(x, slide_id, task))
return svg