def get_measurements_for_good_pipeline(nimages = 1,
group_numbers = None):
'''Get an appropriately initialized measurements structure for the good pipeline'''
path = os.path.join(example_images_directory(), "ExampleSBSImages")
m = cpmeas.Measurements()
if group_numbers is None:
group_numbers = [1] * nimages
group_indexes = [1]
last_group_number = group_numbers[0]
group_index = 1
for group_number in group_numbers:
if group_number == last_group_number:
group_index += 1
else:
group_index = 1
group_indexes.append(group_index)
for i in range(1, nimages+1):
filename = ("Channel2-%02d-%s-%02d.tif" %
(i, "ABCDEFGH"[int((i-1) / 12)], ((i-1) % 12) + 1))
url = pathname2url(os.path.join(path, filename))
m[cpmeas.IMAGE, cpmeas.C_FILE_NAME + "_DNA", i] = filename
m[cpmeas.IMAGE, cpmeas.C_PATH_NAME + "_DNA", i] = path
m[cpmeas.IMAGE, cpmeas.C_URL+"_DNA", i] = url
m[cpmeas.IMAGE, cpmeas.GROUP_NUMBER, i] = group_numbers[i-1]
m[cpmeas.IMAGE, cpmeas.GROUP_INDEX, i] = group_indexes[i-1]
pipeline = cpp.Pipeline()
pipeline.loadtxt(StringIO(GOOD_PIPELINE))
pipeline.write_pipeline_measurement(m)
return m
def run_workspace(self, path, load_as_type,
series = None, index = None, channel = None,
single=False, rescaled=True):
'''Run a workspace to load a file
path - path to the file
load_as_type - one of the LOAD_AS... constants
series, index, channel - pick a plane from within a file
returns the workspace after running
'''
n = N.NamesAndTypes()
n.assignment_method.value = N.ASSIGN_ALL if single else N.ASSIGN_RULES
n.single_image_provider.value = IMAGE_NAME
n.single_load_as_choice.value = load_as_type
n.single_rescale.value = rescaled
n.assignments[0].image_name.value = IMAGE_NAME
n.assignments[0].object_name.value = OBJECTS_NAME
n.assignments[0].load_as_choice.value = load_as_type
n.assignments[0].rescale.value = rescaled
n.module_num = 1
pipeline = cpp.Pipeline()
pipeline.add_module(n)
url = pathname2url(path)
pathname, filename = os.path.split(path)
m = cpmeas.Measurements(mode="memory")
if load_as_type == N.LOAD_AS_OBJECTS:
url_feature = cpmeas.C_OBJECTS_URL + "_" + OBJECTS_NAME
path_feature = cpmeas.C_OBJECTS_PATH_NAME + "_" + OBJECTS_NAME
file_feature = cpmeas.C_OBJECTS_FILE_NAME + "_" + OBJECTS_NAME
series_feature = cpmeas.C_OBJECTS_SERIES + "_" + OBJECTS_NAME
frame_feature = cpmeas.C_OBJECTS_FRAME + "_" + OBJECTS_NAME
channel_feature = cpmeas.C_OBJECTS_CHANNEL + "_" + OBJECTS_NAME
else:
url_feature = cpmeas.C_URL + "_" + IMAGE_NAME
path_feature = cpmeas.C_PATH_NAME + "_" + IMAGE_NAME
file_feature = cpmeas.C_FILE_NAME + "_" + IMAGE_NAME
series_feature = cpmeas.C_SERIES + "_" + IMAGE_NAME
frame_feature = cpmeas.C_FRAME + "_" + IMAGE_NAME
channel_feature = cpmeas.C_CHANNEL + "_" + IMAGE_NAME
m.image_set_number = 1
m.add_measurement(cpmeas.IMAGE, url_feature, url)
m.add_measurement(cpmeas.IMAGE, path_feature, pathname)
m.add_measurement(cpmeas.IMAGE, file_feature, filename)
if series is not None:
m.add_measurement(cpmeas.IMAGE, series_feature, series)
if index is not None:
m.add_measurement(cpmeas.IMAGE, frame_feature, index)
if channel is not None:
m.add_measurement(cpmeas.IMAGE, channel_feature, channel)
m.add_measurement(cpmeas.IMAGE, cpmeas.GROUP_NUMBER, 1)
m.add_measurement(cpmeas.IMAGE, cpmeas.GROUP_INDEX, 1)
workspace = cpw.Workspace(pipeline, n, m,
N.cpo.ObjectSet(),
m, None)
n.run(workspace)
return workspace
def get_measurements_for_good_pipeline(nimages = 1,
group_numbers = None):
'''Get an appropriately initialized measurements structure for the good pipeline'''
path = os.path.join(example_images_directory(), "ExampleSBSImages")
m = cpmeas.Measurements()
if group_numbers is None:
group_numbers = [1] * nimages
group_indexes = [1]
last_group_number = group_numbers[0]
group_index = 1
for group_number in group_numbers:
if group_number == last_group_number:
group_index += 1
else:
group_index = 1
group_indexes.append(group_index)
for i in range(1, nimages+1):
filename = ("Channel2-%02d-%s-%02d.tif" %
(i, "ABCDEFGH"[int((i-1) / 12)], ((i-1) % 12) + 1))
url = pathname2url(os.path.join(path, filename))
m[cpmeas.IMAGE, cpmeas.C_FILE_NAME + "_DNA", i] = filename
m[cpmeas.IMAGE, cpmeas.C_PATH_NAME + "_DNA", i] = path
m[cpmeas.IMAGE, cpmeas.C_URL+"_DNA", i] = url
m[cpmeas.IMAGE, cpmeas.GROUP_NUMBER, i] = group_numbers[i-1]
m[cpmeas.IMAGE, cpmeas.GROUP_INDEX, i] = group_indexes[i-1]
jblob = J.run_script("""
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
var imageFile=new ImageFile(new java.net.URI(url));
var imageFileDetails = new ImageFileDetails(imageFile);
var imageSeries=new ImageSeries(imageFile, 0);
var imageSeriesDetails = new ImageSeriesDetails(imageSeries, imageFileDetails);
var imagePlane=new ImagePlane(imageSeries, 0, ImagePlane.ALWAYS_MONOCHROME);
var ipd = new ImagePlaneDetails(imagePlane, imageSeriesDetails);
var stack = ImagePlaneDetailsStack.makeMonochromeStack(ipd);
var stacks = java.util.Collections.singletonList(stack);
var keys = java.util.Collections.singletonList(imageNumber);
var imageSet = new ImageSet(stacks, keys);
imageSet.compress(java.util.Collections.singletonList("DNA"), null);
""", dict(url=url, imageNumber = str(i)))
blob = J.get_env().get_byte_array_elements(jblob)
m[cpmeas.IMAGE, M_IMAGE_SET, i, blob.dtype] = blob
pipeline = cpp.Pipeline()
pipeline.loadtxt(StringIO(GOOD_PIPELINE))
pipeline.write_pipeline_measurement(m)
return m
def test_04_03_load_planes(self):
file_name = "RLM1 SSN3 300308 008015000.flex"
maybe_download_test_image(file_name)
path = testimages_directory()
pathname = os.path.join(path, file_name)
url = pathname2url(pathname)
ftrs = (cpmeas.C_URL, cpmeas.C_SERIES, cpmeas.C_FRAME)
channels = ("Channel1", "Channel2")
header = ",".join([
",".join(["_".join((ftr, channel)) for ftr in ftrs])
for channel in channels
])
csv_lines = [header]
for series in range(4):
csv_lines.append(",".join([
'"%s","%d","%d"' % (url, series, frame) for frame in range(2)
]))
csv_text = "\n".join(csv_lines)
pipeline, module, filename = self.make_pipeline(csv_text)
assert isinstance(module, L.LoadData)
m = cpmeas.Measurements()
image_set_list = cpi.ImageSetList()
try:
workspace = cpw.Workspace(pipeline, module, m, None, m,
image_set_list)
self.assertTrue(module.prepare_run(workspace))
pixel_hashes = []
for i in range(4):
m.next_image_set(i + 1)
module.run(workspace)
chashes = []
for channel in channels:
pixel_data = m.get_image(channel).pixel_data
h = hashlib.md5()
h.update(pixel_data)
chashes.append(h.digest())
self.assertNotEqual(chashes[0], chashes[1])
for j, ph in enumerate(pixel_hashes):
for k, phh in enumerate(ph):
for l, phd in enumerate(chashes):
self.assertNotEqual(phh, phd)
pixel_hashes.append(chashes)
finally:
os.remove(filename)
def prepare_run(self, workspace):
m = workspace.measurements
assert isinstance(m, cpmeas.Measurements)
root = self.get_base_directory(workspace)
if m.image_set_count == 0:
# Oh bad - using LoadSingleImage to load one image and process it
image_numbers = [1]
else:
image_numbers = m.get_image_numbers()
for image_number in image_numbers:
dict = self.get_file_names(workspace,
image_set_number=image_number)
for image_name in dict.keys():
file_settings = self.get_file_settings(image_name)
if file_settings.image_objects_choice == IO_IMAGES:
#
# Add measurements
#
path_name_category = C_PATH_NAME
file_name_category = C_FILE_NAME
url_category = C_URL
else:
#
# Add measurements
#
path_name_category = C_OBJECTS_PATH_NAME
file_name_category = C_OBJECTS_FILE_NAME
url_category = C_OBJECTS_URL
url = pathname2url(os.path.join(root, dict[image_name]))
for category, value in (
(path_name_category, root),
(file_name_category, dict[image_name]),
(url_category, url),
):
measurement_name = "_".join((category, image_name))
m.add_measurement(
cpmeas.IMAGE,
measurement_name,
value,
image_set_number=image_number,
)
return True
def save_filename_measurements(self, workspace):
if self.update_file_names.value:
filename = self.get_filename(workspace,
make_dirs=False,
check_overwrite=False)
pn, fn = os.path.split(filename)
url = pathname2url(filename)
workspace.measurements.add_measurement(cpmeas.IMAGE,
self.file_name_feature,
fn,
can_overwrite=True)
workspace.measurements.add_measurement(cpmeas.IMAGE,
self.path_name_feature,
pn,
can_overwrite=True)
workspace.measurements.add_measurement(cpmeas.IMAGE,
self.url_feature,
url,
can_overwrite=True)
def test_04_03_load_planes(self):
file_name = "RLM1 SSN3 300308 008015000.flex"
maybe_download_tesst_image(file_name)
path = testimages_directory()
pathname = os.path.join(path, file_name)
url = pathname2url(pathname)
ftrs = (cpmeas.C_URL, cpmeas.C_SERIES, cpmeas.C_FRAME)
channels = ("Channel1", "Channel2")
header = ",".join([",".join(["_".join((ftr, channel)) for ftr in ftrs])
for channel in channels])
csv_lines = [header]
for series in range(4):
csv_lines.append(",".join(['"%s","%d","%d"' % (url, series, frame)
for frame in range(2)]))
csv_text = "\n".join(csv_lines)
pipeline, module, filename = self.make_pipeline(csv_text)
assert isinstance(module, L.LoadData)
m = cpmeas.Measurements()
image_set_list = cpi.ImageSetList()
try:
workspace = cpw.Workspace(pipeline, module, m, None, m,
image_set_list)
self.assertTrue(module.prepare_run(workspace))
pixel_hashes = []
for i in range(4):
m.next_image_set(i+1)
module.run(workspace)
chashes = []
for channel in channels:
pixel_data = m.get_image(channel).pixel_data
h = hashlib.md5()
h.update(pixel_data)
chashes.append(h.digest())
self.assertNotEqual(chashes[0], chashes[1])
for j, ph in enumerate(pixel_hashes):
for k, phh in enumerate(ph):
for l, phd in enumerate(chashes):
self.assertNotEqual(phh, phd)
pixel_hashes.append(chashes)
finally:
os.remove(filename)
def prepare_run(self, workspace):
m = workspace.measurements
assert isinstance(m, cpmeas.Measurements)
root = self.get_base_directory(workspace)
if m.image_set_count == 0:
# Oh bad - using LoadSingleImage to load one image and process it
image_numbers = [1]
else:
image_numbers = m.get_image_numbers()
for image_number in image_numbers:
dict = self.get_file_names(workspace, image_set_number=image_number)
for image_name in dict.keys():
file_settings = self.get_file_settings(image_name)
if file_settings.image_objects_choice == IO_IMAGES:
#
# Add measurements
#
path_name_category = C_PATH_NAME
file_name_category = C_FILE_NAME
url_category = C_URL
else:
#
# Add measurements
#
path_name_category = C_OBJECTS_PATH_NAME
file_name_category = C_OBJECTS_FILE_NAME
url_category = C_OBJECTS_URL
url = pathname2url(os.path.join(root, dict[image_name]))
for category, value in (
(path_name_category, root),
(file_name_category, dict[image_name]),
(url_category, url)):
measurement_name = "_".join((category, image_name))
m.add_measurement(cpmeas.IMAGE, measurement_name, value,
image_set_number=image_number)
return True
def run_as_data_tool(self):
from cellprofiler.gui.editobjectsdlg import EditObjectsDialog
import wx
from wx.lib.filebrowsebutton import FileBrowseButton
from cellprofiler.modules.namesandtypes import ObjectsImageProvider
from bioformats import load_image
with wx.Dialog(None) as dlg:
dlg.Title = "Choose files for editing"
dlg.Sizer = wx.BoxSizer(wx.VERTICAL)
sub_sizer = wx.BoxSizer(wx.HORIZONTAL)
dlg.Sizer.Add(sub_sizer, 0, wx.EXPAND | wx.ALL, 5)
new_or_existing_rb = wx.RadioBox(dlg,
style=wx.RA_VERTICAL,
choices=("New", "Existing"))
sub_sizer.Add(new_or_existing_rb, 0, wx.EXPAND)
objects_file_fbb = FileBrowseButton(
dlg,
size=(300, -1),
fileMask=
"Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg",
dialogTitle="Select objects file",
labelText="Objects file:",
)
objects_file_fbb.Enable(False)
sub_sizer.AddSpacer(5)
sub_sizer.Add(objects_file_fbb, 0, wx.ALIGN_TOP | wx.ALIGN_RIGHT)
def on_radiobox(event):
objects_file_fbb.Enable(new_or_existing_rb.GetSelection() == 1)
new_or_existing_rb.Bind(wx.EVT_RADIOBOX, on_radiobox)
image_file_fbb = FileBrowseButton(
dlg,
size=(300, -1),
fileMask=
"Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg",
dialogTitle="Select guide image file",
labelText="Guide image:",
)
dlg.Sizer.Add(image_file_fbb, 0, wx.EXPAND | wx.ALL, 5)
allow_overlap_checkbox = wx.CheckBox(dlg, -1,
"Allow objects to overlap")
allow_overlap_checkbox.Value = True
dlg.Sizer.Add(allow_overlap_checkbox, 0, wx.EXPAND | wx.ALL, 5)
buttons = wx.StdDialogButtonSizer()
dlg.Sizer.Add(buttons, 0,
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.ALL,
5)
buttons.Add(wx.Button(dlg, wx.ID_OK))
buttons.Add(wx.Button(dlg, wx.ID_CANCEL))
buttons.Realize()
dlg.Fit()
result = dlg.ShowModal()
if result != wx.ID_OK:
return
self.allow_overlap.value = allow_overlap_checkbox.Value
fullname = objects_file_fbb.GetValue()
guidename = image_file_fbb.GetValue()
if new_or_existing_rb.GetSelection() == 1:
provider = ObjectsImageProvider("InputObjects",
pathname2url(fullname), None, None)
image = provider.provide_image(None)
pixel_data = image.pixel_data
shape = pixel_data.shape[:2]
labels = [pixel_data[:, :, i] for i in range(pixel_data.shape[2])]
else:
labels = None
#
# Load the guide image
#
guide_image = load_image(guidename)
if np.min(guide_image) != np.max(guide_image):
guide_image = (guide_image - np.min(guide_image)) / (
np.max(guide_image) - np.min(guide_image))
if labels is None:
shape = guide_image.shape[:2]
labels = [np.zeros(shape, int)]
with EditObjectsDialog(guide_image, labels, self.allow_overlap,
self.object_name.value) as dialog_box:
result = dialog_box.ShowModal()
if result != wx.OK:
return
labels = dialog_box.labels
n_frames = len(labels)
with wx.FileDialog(None,
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) as dlg:
dlg.Path = fullname
dlg.Wildcard = ("Object image file (*.tif,*.tiff)|*.tif;*.tiff|"
"Ilastik project file (*.ilp)|*.ilp")
result = dlg.ShowModal()
fullname = dlg.Path
if result == wx.ID_OK:
if fullname.endswith(".ilp"):
self.save_into_ilp(fullname, labels, guidename)
else:
from bioformats.formatwriter import write_image
from bioformats.omexml import PT_UINT16
if os.path.exists(fullname):
os.unlink(fullname)
for i, l in enumerate(labels):
write_image(fullname,
l,
PT_UINT16,
t=i,
size_t=len(labels))
def run_as_data_tool(self):
from cellprofiler.gui.editobjectsdlg import EditObjectsDialog
import wx
from wx.lib.filebrowsebutton import FileBrowseButton
from cellprofiler.modules.namesandtypes import ObjectsImageProvider
from bioformats import load_image
with wx.Dialog(None) as dlg:
dlg.Title = "Choose files for editing"
dlg.Sizer = wx.BoxSizer(wx.VERTICAL)
box = wx.StaticBox(dlg, -1, "Choose or create new objects file")
sub_sizer = wx.StaticBoxSizer(box, wx.HORIZONTAL)
dlg.Sizer.Add(sub_sizer, 0, wx.EXPAND | wx.ALL, 5)
new_or_existing_rb = wx.RadioBox(dlg, style=wx.RA_VERTICAL,
choices = ("New", "Existing"))
sub_sizer.Add(new_or_existing_rb, 0, wx.EXPAND)
objects_file_fbb = FileBrowseButton(
dlg, size=(300, -1),
fileMask="Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg",
dialogTitle="Select objects file",
labelText="Objects file:")
objects_file_fbb.Enable(False)
sub_sizer.AddSpacer(5)
sub_sizer.Add(objects_file_fbb, 0, wx.ALIGN_TOP | wx.ALIGN_RIGHT)
def on_radiobox(event):
objects_file_fbb.Enable(new_or_existing_rb.GetSelection() == 1)
new_or_existing_rb.Bind(wx.EVT_RADIOBOX, on_radiobox)
image_file_fbb = FileBrowseButton(
dlg, size=(300, -1),
fileMask="Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg",
dialogTitle="Select guide image file",
labelText="Guide image:")
dlg.Sizer.Add(image_file_fbb, 0, wx.EXPAND | wx.ALL, 5)
allow_overlap_checkbox = wx.CheckBox(dlg, -1, "Allow objects to overlap")
allow_overlap_checkbox.Value = True
dlg.Sizer.Add(allow_overlap_checkbox, 0, wx.EXPAND | wx.ALL, 5)
buttons = wx.StdDialogButtonSizer()
dlg.Sizer.Add(buttons, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.ALL, 5)
buttons.Add(wx.Button(dlg, wx.ID_OK))
buttons.Add(wx.Button(dlg, wx.ID_CANCEL))
buttons.Realize()
dlg.Fit()
result = dlg.ShowModal()
if result != wx.ID_OK:
return
self.allow_overlap.value = allow_overlap_checkbox.Value
fullname = objects_file_fbb.GetValue()
guidename = image_file_fbb.GetValue()
if new_or_existing_rb.GetSelection() == 1:
provider = ObjectsImageProvider(
"InputObjects",
pathname2url(fullname),
None, None)
image = provider.provide_image(None)
pixel_data = image.pixel_data
shape = pixel_data.shape[:2]
labels = [pixel_data[:, :, i] for i in range(pixel_data.shape[2])]
else:
labels = None
#
# Load the guide image
#
guide_image = load_image(guidename)
if np.min(guide_image) != np.max(guide_image):
guide_image = ((guide_image - np.min(guide_image)) /
(np.max(guide_image) - np.min(guide_image)))
if labels is None:
shape = guide_image.shape[:2]
labels = [np.zeros(shape, int)]
with EditObjectsDialog(
guide_image, labels,
self.allow_overlap, self.object_name.value) as dialog_box:
result = dialog_box.ShowModal()
if result != wx.OK:
return
labels = dialog_box.labels
n_frames = len(labels)
with wx.FileDialog(None,
style = wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) as dlg:
dlg.Path = fullname
dlg.Wildcard = ("Object image file (*.tif,*.tiff)|*.tif;*.tiff|"
"Ilastik project file (*.ilp)|*.ilp")
result = dlg.ShowModal()
fullname = dlg.Path
if result == wx.ID_OK:
if fullname.endswith(".ilp"):
self.save_into_ilp(fullname, labels, guidename)
else:
from bioformats.formatwriter import write_image
from bioformats.omexml import PT_UINT16
if os.path.exists(fullname):
os.unlink(fullname)
for i, l in enumerate(labels):
write_image(fullname, l, PT_UINT16,
t = i, size_t = len(labels))
def run_create_webpage(self, image_paths, thumb_paths=None,
metadata=None, alter_fn=None):
'''Run the create_webpage module, returning the resulting HTML document
image_paths - list of path / filename tuples. The function will
write an image to each of these and put images and
measurements into the workspace for each.
thumb_paths - if present a list of path / filename tuples. Same as above
metadata - a dictionary of feature / string values
alter_fn - function taking a CreateWebPage module, for you to
alter the module's settings
'''
np.random.seed(0)
module = C.CreateWebPage()
module.module_num = 1
module.orig_image_name.value = IMAGE_NAME
module.web_page_file_name.value = DEFAULT_HTML_FILE
if alter_fn is not None:
alter_fn(module)
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
images = [(IMAGE_NAME, image_paths)]
if thumb_paths:
images += [(THUMB_NAME, thumb_paths)]
self.assertEqual(len(image_paths), len(thumb_paths))
module.wants_thumbnails.value = True
module.thumbnail_image_name.value = THUMB_NAME
else:
module.wants_thumbnails.value = False
measurements = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module,
measurements, None, measurements,
None, None)
for i in range(len(image_paths)):
image_number = i + 1
if metadata is not None:
for key in metadata.keys():
values = metadata[key]
feature = cpmeas.C_METADATA + "_" + key
measurements[cpmeas.IMAGE, feature, image_number] = values[i]
for image_name, paths in images:
pixel_data = np.random.uniform(size=(10, 13))
path_name, file_name = paths[i]
if path_name is None:
path_name = cpprefs.get_default_image_directory()
is_file = True
elif path_name.lower().startswith("http"):
is_file = False
url = path_name + "/" + file_name
if "?" in file_name:
file_name = file_name.split("?", 1)[0]
if is_file:
full_path = os.path.abspath(os.path.join(
self.directory, path_name, file_name))
url = pathname2url(full_path)
path = os.path.split(full_path)[0]
else:
full_path = url
path = path_name
if is_file:
write_image(full_path, pixel_data, PT_UINT8)
path_feature = '_'.join((C_PATH_NAME, image_name))
file_feature = '_'.join((C_FILE_NAME, image_name))
url_feature = '_'.join((C_URL, image_name))
measurements[cpmeas.IMAGE, path_feature, image_number] = \
path
measurements[cpmeas.IMAGE, file_feature, image_number] = \
file_name
measurements[cpmeas.IMAGE, url_feature, image_number] = url
module.post_run(workspace)
return measurements
def run_create_webpage(self, image_paths, thumb_paths = None,
metadata = None, alter_fn = None):
'''Run the create_webpage module, returning the resulting HTML document
image_paths - list of path / filename tuples. The function will
write an image to each of these and put images and
measurements into the workspace for each.
thumb_paths - if present a list of path / filename tuples. Same as above
metadata - a dictionary of feature / string values
alter_fn - function taking a CreateWebPage module, for you to
alter the module's settings
'''
np.random.seed(0)
module = C.CreateWebPage()
module.module_num = 1
module.orig_image_name.value = IMAGE_NAME
module.web_page_file_name.value = DEFAULT_HTML_FILE
if alter_fn is not None:
alter_fn(module)
pipeline = cpp.Pipeline()
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
pipeline.add_listener(callback)
pipeline.add_module(module)
images = [ (IMAGE_NAME, image_paths)]
if thumb_paths:
images += [ (THUMB_NAME, thumb_paths)]
self.assertEqual(len(image_paths), len(thumb_paths))
module.wants_thumbnails.value = True
module.thumbnail_image_name.value = THUMB_NAME
else:
module.wants_thumbnails.value = False
measurements = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module,
measurements, None, measurements,
None, None)
for i in range(len(image_paths)):
image_number = i+1
if metadata is not None:
for key in metadata.keys():
values = metadata[key]
feature = cpmeas.C_METADATA + "_" + key
measurements[cpmeas.IMAGE, feature, image_number] = values[i]
for image_name, paths in images:
pixel_data = np.random.uniform(size=(10,13))
path_name, file_name = paths[i]
if path_name is None:
path_name = cpprefs.get_default_image_directory()
is_file = True
elif path_name.lower().startswith("http"):
is_file = False
url = path_name + "/" + file_name
if "?" in file_name:
file_name = file_name.split("?", 1)[0]
if is_file:
full_path = os.path.abspath(os.path.join(
self.directory, path_name, file_name))
url = pathname2url(full_path)
path = os.path.split(full_path)[0]
else:
full_path = url
path = path_name
if is_file:
write_image(full_path, pixel_data, PT_UINT8)
path_feature = '_'.join((C_PATH_NAME, image_name))
file_feature = '_'.join((C_FILE_NAME, image_name))
url_feature = '_'.join((C_URL, image_name))
measurements[cpmeas.IMAGE, path_feature, image_number] = \
path
measurements[cpmeas.IMAGE, file_feature, image_number] =\
file_name
measurements[cpmeas.IMAGE, url_feature, image_number] = url
module.post_run(workspace)
return measurements