def run(self, workspace):
image_name = self.image_name.value
measurements = workspace.measurements
image_set = workspace.image_set
M_FILE_NAME = cpmeas.C_FILE_NAME + "_" + image_name
M_PATH_NAME = cpmeas.C_PATH_NAME + "_" + image_name
#
# Use measurements.get_measurement to get the file name and path name
# for this cycle
#
path_name = measurements.get_measurement(cpmeas.IMAGE, M_PATH_NAME)
file_name = measurements.get_measurement(cpmeas.IMAGE, M_FILE_NAME)
#
# use os.path.join(pathname, filename) to get the name for BioFormats
#
path = os.path.join(path_name, file_name)
#
# call load_using_bioformats(path) to load the file into a numpy array
#
pixel_data = load_using_bioformats(path)
#
# make a cpi.Image for the image data
#
image = cpi.Image(pixel_data, path_name=path_name, file_name=file_name)
#
# call image_set.add to add the image to the image set
#
image_set.add(image_name, image)
def run(self, workspace):
image_name = self.image_name.value
measurements = workspace.measurements
image_set = workspace.image_set
M_FILE_NAME = cpmeas.C_FILE_NAME + "_" + image_name
M_PATH_NAME = cpmeas.C_PATH_NAME + "_" + image_name
#
# Use measurements.get_measurement to get the file name and path name
# for this cycle
#
path_name = measurements.get_measurement(cpmeas.IMAGE, M_PATH_NAME)
file_name = measurements.get_measurement(cpmeas.IMAGE, M_FILE_NAME)
#
# use os.path.join(pathname, filename) to get the name for BioFormats
#
path = os.path.join(path_name, file_name)
#
# call load_using_bioformats(path) to load the file into a numpy array
#
pixel_data = load_using_bioformats(path)
#
# make a cpi.Image for the image data
#
image = cpi.Image(pixel_data, path_name = path_name, file_name = file_name)
#
# call image_set.add to add the image to the image set
#
image_set.add(image_name, image)
def read_test_image(file_name, **kwargs):
'''Read an image from the test directory
file_name - name of the file within the test directory
**kwargs - arguments passe into load_using_bioformats
'''
from bioformats import load_using_bioformats
path = os.path.join(testimages_directory, file_name)
return load_using_bioformats(path, **kwargs)
def read_test_image(file_name, **kwargs):
'''Read an image from the test directory
file_name - name of the file within the test directory
**kwargs - arguments passe into load_using_bioformats
'''
from bioformats import load_using_bioformats
path = os.path.join(testimages_directory, file_name)
return load_using_bioformats(path, **kwargs)
def read_example_image(folder, file_name, **kwargs):
'''Read an example image from one of the example image directories
folder - folder containing images, e.g. "ExampleFlyImages"
file_name - the name of the file within the folder
**kwargs - any keyword arguments are passed onto load_using_bioformats
'''
from bioformats import load_using_bioformats
path = os.path.join(example_images_directory(), folder, file_name)
return load_using_bioformats(path, **kwargs)
def read_example_image(folder, file_name, **kwargs):
'''Read an example image from one of the example image directories
folder - folder containing images, e.g. "ExampleFlyImages"
file_name - the name of the file within the folder
**kwargs - any keyword arguments are passed onto load_using_bioformats
'''
from bioformats import load_using_bioformats
path = os.path.join(example_images_directory(), folder, file_name)
return load_using_bioformats(path, **kwargs)
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_using_bioformats
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_using_bioformats(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_using_bioformats
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_using_bioformats(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))