def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
cc = self.get_cached_commands()
if (not cc.has_key(command)) or (cc[command] is None):
return []
if not d.has_key(command):
classname = cc[command]
try:
plugin = M.get_plugin(classname)
except:
d[command] = []
return []
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
for field, parameter in fp_in:
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_BOOL:
result += [cps.Binary(label, field.getBoolean(plugin))]
elif field_type == P.FT_INTEGER:
result += [cps.Integer(label, field.getLong(plugin))]
elif field_type == P.FT_FLOAT:
result += [cps.Float(label, field.getDouble(plugin))]
elif field_type == P.FT_STRING:
result += [cps.Text(label, J.to_string(field.get(plugin)))]
else:
assert field_type == P.FT_IMAGE
result += [cps.ImageNameSubscriber(label, "None")]
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
result += [cps.ImageNameProvider(parameter.label() or "",
"Output")]
d[command] = result
else:
result = d[command]
return result
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
if bioformats.USE_IJ2:
node = command.get_selected_leaf()
module_info = node[2]
module = IJ2.wrap_module(module_info.createModule())
context = self.get_context()
display_service = IJ2.get_display_service(context)
display_dictionary = {}
for setting, module_item in d[key]:
field_type = module_item.getType()
if isinstance(setting, cps.ImageNameProvider):
continue
if field_type == IJ2.FT_BOOL:
value = J.make_instance("java/lang/Boolean",
"(Z)V", setting.value)
elif field_type == IJ2.FT_INTEGER:
value = J.make_instance("java/lang/Integer",
"(I)V", setting.value)
elif field_type == IJ2.FT_FLOAT:
value = J.make_instance("java/lang/Double",
"(D)V", setting.value)
elif field_type == IJ2.FT_STRING:
value = setting.value
elif field_type == IJ2.FT_COLOR:
value = IJ2.make_color_rgb_from_html(setting.value)
elif field_type == IJ2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
dataset = IJ2.create_dataset(image.pixel_data,
setting.value)
display = display_service.createDisplay(dataset)
if image.has_mask:
overlay = IJ2.create_overlay(image.mask)
display.displayOverlay(overlay)
value = display
display_dictionary[module_item.getName()] = display
if wants_display:
input_images.append((image_name, image.pixel_data))
module.setInput(module_item.getName(), value)
module_service = IJ2.get_module_service(context)
module_service.run(module)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
name = module_item.getName()
output_name = setting.value
if display_dictionary.has_key(name):
display = display_dictionary[name]
else:
display = IJ2.wrap_display(module.getOutput(name))
ds = display_service.getActiveDataset(display)
pixel_data = ds.get_pixel_data()
image = cpi.Image(pixel_data)
workspace.image_set.add(output_name, image)
if wants_display:
output_images.append((output_name, pixel_data))
for display in display_dictionary.values():
panel = IJ2.wrap_display_panel(display.getDisplayPanel())
panel.close()
else:
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
command = command.value
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
for (field, parameter), setting in zip(fp_in, settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale = True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() { run:function() {
importClass(Packages.imagej.plugin.PlugInFunctions);
PlugInFunctions.runInteractively(plugin);
}};""", dict(plugin=plugin)), True)
else:
J.execute_runnable_in_main_thread(plugin, True)
setting_idx = len(fp_in)
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
if bioformats.USE_IJ2:
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
return []
result = []
inputs = module_info.getInputs()
module = module_info.createModule()
implied_outputs = []
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
value = module_item.getValue(module)
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
description = module_item.getDescription()
if field_type == IJ2.FT_BOOL:
setting = cps.Binary(
label,
J.call(value, "booleanValue", "()Z"),
doc = description)
elif field_type == IJ2.FT_INTEGER:
if minimum is not None:
minimum = J.call(minimum, "intValue", "()I")
if maximum is not None:
maximum = J.call(maximum, "intValue", "()I")
setting = cps.Integer(
label,
J.call(value, "intValue", "()I"),
minval = minimum,
maxval = maximum,
doc = description)
elif field_type == IJ2.FT_FLOAT:
if minimum is not None:
minimum = J.call(minimum, "floatValue", "()F")
if maximum is not None:
maximum = J.call(maximum, "floatValue", "()F")
setting = cps.Float(
label,
J.call(value, "floatValue", "()F"),
minval = minimum,
maxval = maximum,
doc = description)
elif field_type == IJ2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(value)
if choices is not None:
choices = [J.to_string(choice)
for choice
in J.iterate_collection(choices)]
setting = cps.Choice(
label, choices, value, doc = description)
else:
setting = cps.Text(
label, value, doc = description)
elif field_type == IJ2.FT_COLOR:
if value is not None:
value = IJ2.color_rgb_to_html(value)
else:
value = "#ffffff"
setting = cps.Color(label, value, doc = description)
elif field_type == IJ2.FT_IMAGE:
setting = cps.ImageNameSubscriber(
label, "InputImage",
doc = description)
#
# This is a Display for ij2 - the plugin typically
# scribbles all over the display's image. So
# we list it as an output too.
#
implied_outputs.append((
cps.ImageNameProvider(
label, "OutputImage",
doc = description), module_item))
elif field_type == IJ2.FT_OVERLAY:
setting = cps.ObjectNameSubscriber(
label, "ImageJObject",
doc = description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
if field_type == IJ2.FT_IMAGE:
result.append((cps.ImageNameProvider(
label, "ImageJImage",
doc = description), output))
result += implied_outputs
d[key] = result
return [setting for setting, module_info in result]
else:
cc = self.get_cached_commands()
if (not cc.has_key(key)) or (cc[key] is None):
return []
classname = cc[key]
try:
plugin = M.get_plugin(classname)
except:
d[key] = []
return []
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
for field, parameter in fp_in:
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_BOOL:
result += [cps.Binary(label, field.getBoolean(plugin))]
elif field_type == P.FT_INTEGER:
result += [cps.Integer(label, field.getLong(plugin))]
elif field_type == P.FT_FLOAT:
result += [cps.Float(label, field.getDouble(plugin))]
elif field_type == P.FT_STRING:
result += [cps.Text(label, J.to_string(field.get(plugin)))]
else:
assert field_type == P.FT_IMAGE
result += [cps.ImageNameSubscriber(label, "None")]
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
result += [cps.ImageNameProvider(parameter.label() or "",
"Output")]
d[key] = result
elif bioformats.USE_IJ2:
result = [setting for setting, module_info in d[key]]
else:
result = d[key]
return result
import cellprofiler.modules.run_imagej as R
run_tests = (sys.platform.startswith("win"))
INPUT_IMAGE_NAME = "inputimage"
OUTPUT_IMAGE_NAME = "outputimage"
#
# Test for presence of tubeness plugin
#
has_tubeness = False
try:
import imagej.macros as M
commands = M.get_commands()
M.get_plugin('features.Tubeness2_0')
has_tubeness = True
except:
print "The Tubeness plugin isn't loaded - using a simplified pipeline"
class TestRunImageJ(unittest.TestCase):
def test_01_01_load_v1(self):
data = r"""CellProfiler Pipeline: http://www.cellprofiler.org
Version:1
SVNRevision:9954
RunImageJ:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D]
Command or macro?:Command
Command\x3A:Sharpen
Macro\x3A:run("Invert");
Options\x3A:nothing
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
for (field, parameter), setting in zip(fp_in, settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name,
must_be_grayscale = True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.static_call('imagej/plugin/PlugInFunctions', 'runInteractively',
'(Ljava/lang/Runnable)V', plugin)
else:
J.call(plugin, 'run', '()V')
setting_idx = len(fp_in)
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
import cellprofiler.modules.run_imagej as R
from bioformats import USE_IJ2
run_tests = (sys.platform.startswith("win") and not USE_IJ2)
INPUT_IMAGE_NAME = "inputimage"
OUTPUT_IMAGE_NAME = "outputimage"
#
# Test for presence of tubeness plugin
#
has_tubeness = False
try:
import imagej.macros as M
commands = M.get_commands()
M.get_plugin('features.Tubeness2_0')
has_tubeness = True
except:
print "The Tubeness plugin isn't loaded - using a simplified pipeline"
class TestRunImageJ(unittest.TestCase):
def test_01_01_load_v1(self):
data = r"""CellProfiler Pipeline: http://www.cellprofiler.org
Version:1
SVNRevision:9954
RunImageJ:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D]
Command or macro?:Command
Command\x3A:Sharpen
Macro\x3A:run("Invert");
def execute_advanced_command(self, workspace, command, d):
'''Execute an advanced command
command - name of the command
d - dictionary to be used to find settings
'''
wants_display = workspace.frame is not None
if wants_display:
workspace.display_data.input_images = input_images = []
workspace.display_data.output_images = output_images = []
key = command.get_unicode_value()
if bioformats.USE_IJ2:
node = command.get_selected_leaf()
module_info = node[2]
module = IJ2.wrap_module(module_info.createModule())
context = self.get_context()
display_service = IJ2.get_display_service(context)
display_dictionary = {}
for setting, module_item in d[key]:
field_type = module_item.getType()
if isinstance(setting, cps.ImageNameProvider):
continue
if field_type == IJ2.FT_BOOL:
value = J.make_instance("java/lang/Boolean", "(Z)V",
setting.value)
elif field_type == IJ2.FT_INTEGER:
value = J.make_instance("java/lang/Integer", "(I)V",
setting.value)
elif field_type == IJ2.FT_FLOAT:
value = J.make_instance("java/lang/Double", "(D)V",
setting.value)
elif field_type == IJ2.FT_STRING:
value = setting.value
elif field_type == IJ2.FT_COLOR:
value = IJ2.make_color_rgb_from_html(setting.value)
elif field_type == IJ2.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(image_name)
dataset = IJ2.create_dataset(image.pixel_data,
setting.value)
display = display_service.createDisplay(dataset)
if image.has_mask:
overlay = IJ2.create_overlay(image.mask)
display.displayOverlay(overlay)
value = display
display_dictionary[module_item.getName()] = display
if wants_display:
input_images.append((image_name, image.pixel_data))
module.setInput(module_item.getName(), value)
module_service = IJ2.get_module_service(context)
module_service.run(module)
for setting, module_item in d[key]:
if isinstance(setting, cps.ImageNameProvider):
name = module_item.getName()
output_name = setting.value
if display_dictionary.has_key(name):
display = display_dictionary[name]
else:
display = IJ2.wrap_display(module.getOutput(name))
ds = display_service.getActiveDataset(display)
pixel_data = ds.get_pixel_data()
image = cpi.Image(pixel_data)
workspace.image_set.add(output_name, image)
if wants_display:
output_images.append((output_name, pixel_data))
for display in display_dictionary.values():
panel = IJ2.wrap_display_panel(display.getDisplayPanel())
panel.close()
else:
from imagej.imageplus import make_imageplus_from_processor
from imagej.imageplus import get_imageplus_wrapper
from imagej.imageprocessor import make_image_processor
from imagej.imageprocessor import get_image
command = command.value
settings = d[command]
classname = self.get_cached_commands()[command]
plugin = M.get_plugin(classname)
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
for (field, parameter), setting in zip(fp_in,
settings[:len(fp_in)]):
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_IMAGE:
image_name = setting.value
image = workspace.image_set.get_image(
image_name, must_be_grayscale=True)
pixel_data = (image.pixel_data * 255.0).astype(np.float32)
if wants_display:
input_images.append((image_name, pixel_data / 255.0))
processor = make_image_processor(pixel_data)
image_plus = make_imageplus_from_processor(
image_name, processor)
field.set(plugin, image_plus)
del image_plus
del processor
elif field_type == P.FT_INTEGER:
field.setInt(plugin, setting.value)
elif field_type == P.FT_FLOAT:
field.setFloat(plugin, setting.value)
elif field_type == P.FT_BOOL:
field.setBoolean(plugin, setting.value)
else:
field.set(plugin, setting.value)
#
# There are two ways to run this:
# * Batch - just call plugin.run()
# * Interactive - use PlugInFunctions.runInteractively
#
if self.pause_before_proceeding:
J.static_call('imagej/plugin/PlugInFunctions',
'runInteractively', '(Ljava/lang/Runnable)V',
plugin)
else:
J.call(plugin, 'run', '()V')
setting_idx = len(fp_in)
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
image_name = settings[setting_idx].value
setting_idx += 1
image_plus = get_imageplus_wrapper(field.get(plugin))
processor = image_plus.getProcessor()
pixel_data = get_image(processor).astype(
np.float32) / 255.0
if wants_display:
output_images.append((image_name, pixel_data))
image = cpi.Image(pixel_data)
image_set.add(image_name, image)
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
if bioformats.USE_IJ2:
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
return []
result = []
inputs = module_info.getInputs()
module = module_info.createModule()
implied_outputs = []
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
value = module_item.getValue(module)
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
description = module_item.getDescription()
if field_type == IJ2.FT_BOOL:
setting = cps.Binary(label,
J.call(value, "booleanValue",
"()Z"),
doc=description)
elif field_type == IJ2.FT_INTEGER:
if minimum is not None:
minimum = J.call(minimum, "intValue", "()I")
if maximum is not None:
maximum = J.call(maximum, "intValue", "()I")
setting = cps.Integer(label,
J.call(value, "intValue", "()I"),
minval=minimum,
maxval=maximum,
doc=description)
elif field_type == IJ2.FT_FLOAT:
if minimum is not None:
minimum = J.call(minimum, "floatValue", "()F")
if maximum is not None:
maximum = J.call(maximum, "floatValue", "()F")
setting = cps.Float(label,
J.call(value, "floatValue", "()F"),
minval=minimum,
maxval=maximum,
doc=description)
elif field_type == IJ2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(value)
if choices is not None:
choices = [
J.to_string(choice)
for choice in J.iterate_collection(choices)
]
setting = cps.Choice(label,
choices,
value,
doc=description)
else:
setting = cps.Text(label, value, doc=description)
elif field_type == IJ2.FT_COLOR:
if value is not None:
value = IJ2.color_rgb_to_html(value)
else:
value = "#ffffff"
setting = cps.Color(label, value, doc=description)
elif field_type == IJ2.FT_IMAGE:
setting = cps.ImageNameSubscriber(label,
"InputImage",
doc=description)
#
# This is a Display for ij2 - the plugin typically
# scribbles all over the display's image. So
# we list it as an output too.
#
implied_outputs.append(
(cps.ImageNameProvider(label,
"OutputImage",
doc=description),
module_item))
elif field_type == IJ2.FT_OVERLAY:
setting = cps.ObjectNameSubscriber(label,
"ImageJObject",
doc=description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
if field_type == IJ2.FT_IMAGE:
result.append(
(cps.ImageNameProvider(label,
"ImageJImage",
doc=description), output))
result += implied_outputs
d[key] = result
return [setting for setting, module_info in result]
else:
cc = self.get_cached_commands()
if (not cc.has_key(key)) or (cc[key] is None):
return []
classname = cc[key]
try:
plugin = M.get_plugin(classname)
except:
d[key] = []
return []
fp_in = P.get_input_fields_and_parameters(plugin)
result = []
for field, parameter in fp_in:
field_type = P.get_field_type(field)
label = parameter.label() or ""
if field_type == P.FT_BOOL:
result += [cps.Binary(label, field.getBoolean(plugin))]
elif field_type == P.FT_INTEGER:
result += [cps.Integer(label, field.getLong(plugin))]
elif field_type == P.FT_FLOAT:
result += [cps.Float(label, field.getDouble(plugin))]
elif field_type == P.FT_STRING:
result += [
cps.Text(label, J.to_string(field.get(plugin)))
]
else:
assert field_type == P.FT_IMAGE
result += [cps.ImageNameSubscriber(label, "None")]
fp_out = P.get_output_fields_and_parameters(plugin)
for field, parameter in fp_out:
field_type = P.get_field_type(field)
if field_type == P.FT_IMAGE:
result += [
cps.ImageNameProvider(parameter.label() or "",
"Output")
]
d[key] = result
elif bioformats.USE_IJ2:
result = [setting for setting, module_info in d[key]]
else:
result = d[key]
return result