def test_06_get_settings_list(self):
module1 = instantiate_module("IdentifyPrimaryObjects")
module1.module_num = 1
module2 = instantiate_module("Smooth")
module2.module_num = 2
module3 = instantiate_module("Resize")
module3.module_num = 3
module4 = self.make_instance()
module4.module_num = 4
module4.parameters[0].module_names.value = "IdentifyPrimaryObjects #1"
module4.add_parameter()
module4.parameters[1].module_names.value = "Smooth #2"
module4.add_parameter()
module4.parameters[2].module_names.value = "Resize #3"
module4.add_parameter()
module4.parameters[3].module_names.value = "BayesianOptimisation #4"
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_module(module1)
pipeline.add_module(module2)
pipeline.add_module(module3)
pipeline.add_module(module4)
settings_list = module4.get_settings_from_modules(pipeline)
self.assertTrue("Use advanced settings?" in settings_list)
self.assertTrue("Select smoothing method" in settings_list)
self.assertTrue("Resizing factor" in settings_list)
self.assertTrue("No. of settings to be adjusted" in settings_list)
def test_01_04_instantiate_all(self):
'''Instantiate each module and make sure none import wx'''
import cellprofiler.modules as M
for name in M.get_module_names():
try:
M.instantiate_module(name)
except:
print "Module %s probably imports wx" % name
traceback.print_exc()
def test_01_04_instantiate_all(self):
'''Instantiate each module and make sure none import wx'''
import cellprofiler.modules as M
for name in M.get_module_names():
try:
M.instantiate_module(name)
except:
print "Module %s probably imports wx" % name
traceback.print_exc()
def print_code_statistics():
'''Print # lines of code, # modules, etc to console
This is the official source of code statistics for things like grants.
'''
from cellprofiler.modules import builtin_modules, all_modules, instantiate_module
import subprocess
print "\n\n\n**** CellProfiler code statistics ****"
print "# of built-in modules: %d" % len(builtin_modules)
setting_count = 0
for module in all_modules.values():
if module.__module__.find(".") < 0:
continue
mn = module.__module__.rsplit(".", 1)[1]
if mn not in builtin_modules:
continue
module_instance = instantiate_module(module.module_name)
setting_count += len(module_instance.help_settings())
print "# of settings: %d" % setting_count
filelist = subprocess.Popen(["git", "ls-files"], stdout=subprocess.PIPE).communicate()[0].split("\n")
linecount = 0
for filename in filelist:
if (os.path.exists(filename) and
any([filename.endswith(x) for x in ".py", ".c", ".pyx", ".java"])):
with open(filename, "r") as fd:
linecount += len(fd.readlines())
def output_module_html(webpage_path):
'''Output an HTML page for each module'''
icons_relpath = relpath(cellprofiler.icons.__path__[0])
all_png_icons = glob(os.path.join(icons_relpath, "*.png"))
icon_names = [os.path.basename(f)[:-4] for f in all_png_icons]
help_text = """
<h2>Help for CellProfiler Modules</a></h2>
<ul>\n"""
d = {}
module_path = webpage_path
if not (os.path.exists(module_path) and os.path.isdir(module_path)):
try:
os.mkdir(module_path)
except IOError:
raise ValueError("Could not create directory %s" % module_path)
for module_name in sorted(get_module_names()):
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
if isinstance(module.category, (str,unicode)):
module.category = [module.category]
for category in module.category:
if not d.has_key(category):
d[category] = {}
d[category][module_name] = module
result = module.get_help()
if result is None:
continue
result = result.replace('<body><h1>','<body><h1>Module: ')
# Replace refs to icons in memory with the relative path to the image dir (see above)
result = re.sub("memory:",os.path.join("images","").encode('string-escape'),result)
# Check if a corresponding image exists for the module
if module_name in icon_names:
# Strip out end html tags so I can add more stuff
result = result.replace('</body>','').replace('</html>','')
# Include images specific to the module, relative to html files ('images' dir)
LOCATION_MODULE_IMAGES = os.path.join('images','%s.png'%(module_name))
result += '\n\n<div><p><img src="%s", width="50%%"></p></div>\n'%LOCATION_MODULE_IMAGES
# Now end the help text
result += '</body></html>'
fd = open(os.path.join(module_path,"%s.html" % module_name), "w")
fd.write(result)
fd.close()
for category in sorted(d.keys()):
sub_d = d[category]
help_text += "<li><b>%s</b><br><ul>\n"%category
for module_name in sorted(sub_d.keys()):
help_text += "<li><a href='%s.html'>%s</a></li>\n" % (module_name, module_name)
help_text += "</ul></li>\n"
help_text += "</ul>\n"
return help_text
def print_code_statistics():
'''Print # lines of code, # modules, etc to console
This is the official source of code statistics for things like grants.
'''
from cellprofiler.modules import builtin_modules, all_modules, instantiate_module
import subprocess
print "\n\n\n**** CellProfiler code statistics ****"
print "# of built-in modules: %d" % len(builtin_modules)
setting_count = 0
for module in all_modules.values():
if module.__module__.find(".") < 0:
continue
mn = module.__module__.rsplit(".", 1)[1]
if mn not in builtin_modules:
continue
module_instance = instantiate_module(module.module_name)
setting_count += len(module_instance.help_settings())
print "# of settings: %d" % setting_count
filelist = subprocess.Popen(
["git", "ls-files"],
stdout=subprocess.PIPE).communicate()[0].split("\n")
linecount = 0
for filename in filelist:
if (os.path.exists(filename) and any(
[filename.endswith(x) for x in ".py", ".c", ".pyx", ".java"])):
with open(filename, "r") as fd:
linecount += len(fd.readlines())
def output_module_html(webpage_path):
'''Output an HTML page for each module'''
icons_relpath = relpath(cellprofiler.icons.__path__[0])
all_png_icons = glob(os.path.join(icons_relpath, "*.png"))
icon_names = [os.path.basename(f)[:-4] for f in all_png_icons]
help_text = """
<h2>Help for CellProfiler Modules</a></h2>
<ul>\n"""
d = {}
module_path = webpage_path
if not (os.path.exists(module_path) and os.path.isdir(module_path)):
try:
os.mkdir(module_path)
except IOError:
raise ValueError("Could not create directory %s" % module_path)
for module_name in sorted(get_module_names()):
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
if isinstance(module.category, (str,unicode)):
module.category = [module.category]
for category in module.category:
if not d.has_key(category):
d[category] = {}
d[category][module_name] = module
result = module.get_help()
if result is None:
continue
result = result.replace('<body><h1>','<body><h1>Module: ')
# Replace refs to icons in memory with the relative path to the image dir (see above)
result = re.sub("memory:",os.path.join("images","").encode('string-escape'),result)
# Check if a corresponding image exists for the module
if module_name in icon_names:
# Strip out end html tags so I can add more stuff
result = result.replace('</body>','').replace('</html>','')
# Include images specific to the module, relative to html files ('images' dir)
LOCATION_MODULE_IMAGES = os.path.join('images','%s.png'%(module_name))
result += '\n\n<div><p><img src="%s", width="50%%"></p></div>\n'%LOCATION_MODULE_IMAGES
# Now end the help text
result += '</body></html>'
fd = open(os.path.join(module_path,"%s.html" % module_name), "w")
fd.write(result)
fd.close()
for category in sorted(d.keys()):
sub_d = d[category]
help_text += "<li><b>%s</b><br><ul>\n"%category
for module_name in sorted(sub_d.keys()):
help_text += "<li><a href='%s.html'>%s</a></li>\n" % (module_name, module_name)
help_text += "</ul></li>\n"
help_text += "</ul>\n"
return help_text
def print_code_statistics():
"""Print # lines of code, # modules, etc to console
This is the official source of code statistics for things like grants.
"""
from cellprofiler.modules import builtin_modules, all_modules, instantiate_module
import subprocess
print "\n\n\n**** CellProfiler code statistics ****"
print "# of built-in modules: %d" % len(builtin_modules)
setting_count = 0
for module in all_modules.values():
if module.__module__.find(".") < 0:
continue
mn = module.__module__.rsplit(".", 1)[1]
if mn not in builtin_modules:
continue
module_instance = instantiate_module(module.module_name)
setting_count += len(module_instance.help_settings())
directory = os.path.abspath(os.path.split(sys.argv[0])[0])
try:
filelist = (
subprocess.Popen(["git", "ls-files"], stdout=subprocess.PIPE, cwd=directory).communicate()[0].split("\n")
)
except:
filelist = []
for root, dirs, files in os.walk(directory):
filelist += [os.path.join(root, f) for f in files]
linecount = 0
for filename in filelist:
if os.path.exists(filename) and any([filename.endswith(x) for x in ".py", ".c", ".pyx", ".java"]):
def setUpClass(self):
self.module = instantiate_module(MODULE_NAME)
self.module.input_image_name.value = INPUT_IMAGE_NAME
self.module.output_image_name.value = OUTPUT_IMAGE_NAME
self.module.module_num = 1
self.pipeline = cpp.Pipeline()
self.pipeline.add_module(self.module)
self.package = __import__(self.module.__class__.__module__)
def test_02_01_maybe_you_implemented_get_categories(self):
module = instantiate_module(MODULE_NAME)
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
if module.get_categories.im_func is not cpm.CPModule.get_categories.im_func:
c_image = module.get_categories(None, cpmeas.IMAGE)
self.assertTrue(I.C_COUNT in c_image)
c_objects = module.get_categories(None, OUTPUT_OBJECTS_NAME)
self.assertTrue(I.C_LOCATION in c_objects)
print "+3 for you!"
def test_02_01_maybe_you_implemented_get_categories(self):
module = instantiate_module(MODULE_NAME)
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
if module.get_categories.im_func is not cpm.CPModule.get_categories.im_func:
c_image = module.get_categories(None, cpmeas.IMAGE)
self.assertTrue(I.C_COUNT in c_image)
c_objects = module.get_categories(None, OUTPUT_OBJECTS_NAME)
self.assertTrue(I.C_LOCATION in c_objects)
print "+3 for you!"
def test_02_02_maybe_you_implemented_get_measurements(self):
module = instantiate_module(MODULE_NAME)
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
if module.get_measurements.im_func is not cpm.CPModule.get_measurements.im_func:
ftr_image = module.get_measurements(None, cpmeas.IMAGE, I.C_COUNT)
self.assertTrue(OUTPUT_OBJECTS_NAME in ftr_image)
ftr_objects = module.get_measurements(None, OUTPUT_OBJECTS_NAME,
I.C_LOCATION)
self.assertTrue(I.FTR_CENTER_X in ftr_objects)
self.assertTrue(I.FTR_CENTER_Y in ftr_objects)
print "+3 for you!"
def test_02_02_maybe_you_implemented_get_measurements(self):
module = instantiate_module(MODULE_NAME)
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
if module.get_measurements.im_func is not cpm.CPModule.get_measurements.im_func:
ftr_image = module.get_measurements(None, cpmeas.IMAGE, I.C_COUNT)
self.assertTrue(OUTPUT_OBJECTS_NAME in ftr_image)
ftr_objects = module.get_measurements(None, OUTPUT_OBJECTS_NAME,
I.C_LOCATION)
self.assertTrue(I.FTR_CENTER_X in ftr_objects)
self.assertTrue(I.FTR_CENTER_Y in ftr_objects)
print "+3 for you!"
def setUpClass(cls):
cls.tempdir = tempfile.mkdtemp()
cls.module = instantiate_module(MODULE_NAME)
cls.module.image_name.value = IMAGE_NAME
cls.module.folder.set_dir_choice(cps.ABSOLUTE_FOLDER_NAME)
cls.module.folder.set_custom_path(cls.tempdir)
cls.module.module_num = 1
cls.pipeline = cpp.Pipeline()
cls.pipeline.add_module(cls.module)
for name, data in ((IMAGE_1_NAME, TIF_1), (IMAGE_2_NAME, TIF_2)):
fd = open(os.path.join(cls.tempdir, name), "wb")
fd.write(data)
fd.close()
def test_05_get_module_list(self):
module1 = instantiate_module("IdentifyPrimaryObjects")
module1.module_num = 1
module2 = instantiate_module("Smooth")
module2.module_num = 2
module3 = instantiate_module("Resize")
module3.module_num = 3
module4 = self.make_instance()
module4.module_num = 4
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_module(module1)
pipeline.add_module(module2)
pipeline.add_module(module3)
pipeline.add_module(module4)
module_list = module4.get_module_list(pipeline)
self.assertEqual(len(module_list), 4)
self.assertEqual(module_list[0], "IdentifyPrimaryObjects #1")
self.assertEqual(module_list[1], "Smooth #2")
self.assertEqual(module_list[2], "Resize #3")
self.assertEqual(module_list[3], "BayesianOptimisation #4")
def setUpClass(cls):
cls.tempdir = tempfile.mkdtemp()
cls.module = instantiate_module(MODULE_NAME)
cls.module.image_name.value = IMAGE_NAME
cls.module.folder.set_dir_choice(cps.ABSOLUTE_FOLDER_NAME)
cls.module.folder.set_custom_path(cls.tempdir)
cls.module.module_num = 1
cls.pipeline = cpp.Pipeline()
cls.pipeline.add_module(cls.module)
for name, data in ((IMAGE_1_NAME, TIF_1),
(IMAGE_2_NAME, TIF_2)):
fd = open(os.path.join(cls.tempdir, name), "wb")
fd.write(data)
fd.close()
def test_01_02_run(self):
module = instantiate_module(MODULE_NAME)
module.input_objects_name.value = INPUT_OBJECTS_NAME
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
module.module_num = 1
pipeline = cpp.Pipeline()
pipeline.add_module(module)
object_set = cpo.ObjectSet()
#
# Pick a bunch of random points, dilate them using the distance
# transform and then label the result.
#
r = np.random.RandomState()
r.seed(12)
bimg = np.ones((100, 100), bool)
bimg[r.randint(0,100, 50), r.randint(0, 100, 50)] = False
labels, count = label(distance_transform_edt(bimg) <= 5)
#
# Make the input objects
#
input_objects = cpo.Objects()
input_objects.segmented = labels
expected = skeletonize_labels(labels)
object_set.add_objects(input_objects, INPUT_OBJECTS_NAME)
#
# Make the workspace
#
workspace = cpw.Workspace(pipeline, module, None, object_set,
cpmeas.Measurements(), None)
module.run(workspace)
self.assertTrue(OUTPUT_OBJECTS_NAME in object_set.object_names,
"Could not find the output objects in the object set")
output_objects = object_set.get_objects(OUTPUT_OBJECTS_NAME)
np.testing.assert_array_equal(expected, output_objects.segmented)
def run_tteesstt(self, objects, level):
module = instantiate_module(MODULE_NAME)
module.objects_name.value = OBJECTS_NAME
module.module_num = 1
pipeline = cpp.Pipeline()
pipeline.add_module(module)
object_set = cpo.ObjectSet()
object_set.add_objects(objects, OBJECTS_NAME)
#
# Make the workspace
#
measurements = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module, None, object_set,
measurements, None)
module.run(workspace)
values = measurements.get_measurement(OBJECTS_NAME, "Example5_MeanDistance")
self.assertEqual(len(values), objects.count)
for labels, indices in objects.get_labels():
for l in np.unique(labels):
#
# Test very slowly = 1 object per pass
#
if l == 0:
continue
d = scipy.ndimage.distance_transform_edt(labels == l)
value = np.sum(d) / np.sum(labels == l)
if abs(value - values[l-1]) > .0001:
if level == 1:
self.fail("You got the wrong answer (label = %d, mine = %f, yours = %f" %
l, value, values[l-1])
else:
sys.stderr.write("Oh too bad, did not pass level %d\n" % level)
return
if level > 1:
print "+%d for you!" % level
def test_01_02_run(self):
module = instantiate_module(MODULE_NAME)
module.input_objects_name.value = INPUT_OBJECTS_NAME
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
module.module_num = 1
pipeline = cpp.Pipeline()
pipeline.add_module(module)
object_set = cpo.ObjectSet()
#
# Pick a bunch of random points, dilate them using the distance
# transform and then label the result.
#
r = np.random.RandomState()
r.seed(12)
bimg = np.ones((100, 100), bool)
bimg[r.randint(0,100, 50), r.randint(0, 100, 50)] = False
labels, count = label(distance_transform_edt(bimg) <= 5)
#
# Make the input objects
#
input_objects = cpo.Objects()
input_objects.segmented = labels
expected = skeletonize_labels(labels)
object_set.add_objects(input_objects, INPUT_OBJECTS_NAME)
#
# Make the workspace
#
workspace = cpw.Workspace(pipeline, module, None, object_set,
cpmeas.Measurements(), None)
module.run(workspace)
self.assertTrue(OUTPUT_OBJECTS_NAME in object_set.object_names,
"Could not find the output objects in the object set")
output_objects = object_set.get_objects(OUTPUT_OBJECTS_NAME)
np.testing.assert_array_equal(expected, output_objects.segmented)
def print_code_statistics():
'''Print # lines of code, # modules, etc to console
This is the official source of code statistics for things like grants.
'''
from cellprofiler.modules import builtin_modules, all_modules, instantiate_module
import subprocess
print "\n\n\n**** CellProfiler code statistics ****"
print "# of built-in modules: %d" % len(builtin_modules)
setting_count = 0
for module in all_modules.values():
if module.__module__.find(".") < 0:
continue
mn = module.__module__.rsplit(".", 1)[1]
if mn not in builtin_modules:
continue
module_instance = instantiate_module(module.module_name)
setting_count += len(module_instance.help_settings())
directory = os.path.abspath(os.path.split(sys.argv[0])[0])
try:
filelist = subprocess.Popen(["git", "ls-files"],
stdout=subprocess.PIPE,
cwd=directory).communicate()[0].split("\n")
except:
filelist = []
for root, dirs, files in os.walk(directory):
filelist += [os.path.join(root, f) for f in files]
linecount = 0
for filename in filelist:
if (os.path.exists(filename) and any(
[filename.endswith(x) for x in ".py", ".c", ".pyx", ".java"])):
if filename.endswith(".c") and os.path.exists(filename[:-1] +
"pyx"):
continue
with open(filename, "r") as fd:
linecount += len(fd.readlines())
import cellprofiler.cpimage as cpi
import cellprofiler.measurements as cpm
import cellprofiler.modules.run_imagej as R
import cellprofiler.objects as cpo
import cellprofiler.pipeline as cpp
import cellprofiler.settings as cps
import cellprofiler.workspace as cpw
import imagej.imagej2 as ij2
INPUT_IMAGE_NAME = "inputimage"
OUTPUT_IMAGE_NAME = "outputimage"
from cellprofiler.modules import instantiate_module
try:
instantiate_module("RunImageJ")
skip_tests = False
except:
skip_tests = True
@unittest.skipIf(skip_tests, "RunImageJ did not load (headless?)")
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
def test_01_01_output_module_html(self):
from cellprofiler.modules import get_module_names, instantiate_module
M.output_module_html(self.temp_dir)
for module_name in sorted(get_module_names()):
fd = None
try:
fd = open(os.path.join(self.temp_dir, module_name + ".html"))
except:
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
traceback.print_exc()
self.assert_("Failed to open %s.html" %module_name)
data = fd.read()
fd.close()
#
# Make sure that some nesting rules are obeyed.
#
tags_we_care_about = ("i","b","ul","ol","li","table","tr","td","th",
"h1","h2","h3","html","head", "body")
pattern = r"<\s*([a-zA-Z0-9]+).[^>]*>"
anti_pattern = r"</\s*([a-zA-Z0-9]+)[^>]*>"
d = {}
anti_d = {}
COUNT = 0
LIST = 1
for tag in tags_we_care_about:
for dd in (d, anti_d):
dd[tag] = [0, []]
for p, dd in ((pattern, d),
(anti_pattern, anti_d)):
pos = 0
while(True):
m = re.search(p, data[pos:])
if m is None:
break
tag = m.groups()[0].lower()
pos = pos + m.start(1)+1
if dd.has_key(tag):
dd[tag][COUNT] += 1
dd[tag][LIST].append(pos)
#
# Check table nesting rules
#
T_TABLE = 0
T_ANTI_TABLE = 1
T_TR = 2
T_ANTI_TR = 3
T_TH = 4
T_ANTI_TH = 5
T_TD = 6
T_ANTI_TD = 7
T_UL = 8
T_ANTI_UL = 9
T_OL = 10
T_ANTI_OL = 11
T_LI = 12
T_ANTI_LI = 13
T_I = 14
T_ANTI_I = 15
T_B = 16
T_ANTI_B = 17
tokens = []
for tag, token, anti_token in (
('table', T_TABLE, T_ANTI_TABLE),
('tr', T_TR, T_ANTI_TR),
('td', T_TD, T_ANTI_TD),
('th', T_TH, T_ANTI_TH),
('ul', T_UL, T_ANTI_UL),
('ol', T_OL, T_ANTI_OL),
('li', T_LI, T_ANTI_LI),
('i', T_I, T_ANTI_I),
('b', T_B, T_ANTI_B)
):
tokens += [(pos, token) for pos in d[tag][LIST]]
tokens += [(pos, anti_token) for pos in anti_d[tag][LIST]]
tokens = sorted(tokens)
S_INIT = 0
S_AFTER_TABLE = 1
S_AFTER_TR = 2
S_AFTER_TD = 3
S_AFTER_TH = 4
S_AFTER_OL = 5
S_AFTER_UL = 6
S_AFTER_LI = 7
S_AFTER_I = 8
S_AFTER_B = 9
state_transitions = {
S_INIT: { T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_I: S_AFTER_I,
T_B: S_AFTER_B },
S_AFTER_TABLE: {
T_ANTI_TABLE: S_INIT,
T_TR: S_AFTER_TR
},
S_AFTER_TR: {
T_ANTI_TR: S_INIT,
T_TD: S_AFTER_TD,
T_TH: S_AFTER_TH
},
S_AFTER_TD: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_ANTI_TD: S_INIT
},
S_AFTER_TH: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_ANTI_TH: S_INIT
},
S_AFTER_OL: {
T_LI: S_AFTER_LI,
T_ANTI_OL: S_INIT
},
S_AFTER_UL: {
T_LI: S_AFTER_LI,
T_ANTI_UL: S_INIT
},
S_AFTER_LI: {
T_ANTI_LI: S_INIT,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I
},
S_AFTER_I: {
T_ANTI_I: S_INIT,
T_I: S_AFTER_I, # Stupid but legal <i><i>Foo</i></i>
T_B: S_AFTER_B,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL
},
S_AFTER_B: {
T_ANTI_B: S_INIT,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL
}
}
state = []
for pos, token in tokens:
self.assertTrue(
len(state) >= 0,
"Error in %s near position %d (%s)" %
(module_name, pos, data[max(0,pos - 30):
max(pos + 30, len(data))])
)
top_state, start_pos = (S_INIT,0) if len(state) == 0 else state[-1]
self.assertTrue(
state_transitions[top_state].has_key(token),
"Nesting error in %s near position %d (%s)" %
(module_name, pos, data[max(0,pos - 50):pos]+"^^^"+
data[pos:min(pos + 50, len(data))]))
next_state = state_transitions[top_state][token]
if next_state == S_INIT:
state.pop()
else:
state.append((next_state, pos))
if len(state) > 0:
self.assertEqual(
len(state), 0,
"Couldn't find last closing tag in %s. Last tag position = %d (%s)" %
(module_name, state[-1][1], data[(state[-1][1] - 30):
(state[-1][1] + 30)]))
#
# Check begin/end tag counts
#
for tag in tags_we_care_about:
if d.has_key(tag):
self.assertTrue(anti_d.has_key(tag),
"Missing closing </%s> tag in %s" %
(tag, module_name))
self.assertEqual(
d[tag][COUNT], anti_d[tag][COUNT],
"Found %d <%s>, != %d </%s> in %s" %
(d[tag][COUNT], tag,
anti_d[tag][COUNT], tag, module_name))
else:
self.assertFalse(anti_d.has_key(tag),
"Missing opening <%s> tag in %s" %
(tag, module_name))
def make_instance(self):
'''Return an instance of example1 this way because it's not on classpath'''
return instantiate_module("Example1b")
def make_instance(self):
return instantiate_module("Example2a")
def test_01_01_instantiate(self):
try:
instantiate_module(MODULE_NAME)
except:
self.fail("CellProfiler could not create your module. "
"Is it named, " + MODULE_NAME + "?")
def __init__(self, *args, **kwds):
'''Instantiate a data tool frame
module_name: name of module to instantiate
measurements_file_name: name of measurements file
'''
assert kwds.has_key("module_name"), "DataToolFrame() needs a module_name argument"
assert kwds.has_key("measurements_file_name"), "DataToolFrame() needs a measurements_file_name argument"
module_name = kwds["module_name"]
measurements_file_name = kwds["measurements_file_name"]
kwds_copy = kwds.copy()
del kwds_copy["module_name"]
del kwds_copy["measurements_file_name"]
kwds_copy["title"]="%s data tool"%module_name
wx.Frame.__init__(self, *args, **kwds_copy)
self.module = instantiate_module(module_name)
self.pipeline = cpp.Pipeline()
if h5py.is_hdf5(measurements_file_name):
self.workspace = cpw.Workspace(self.pipeline, self.module, None, None, None,
None)
self.workspace.load(measurements_file_name, True)
self.measurements = self.workspace.measurements
else:
self.pipeline.load(measurements_file_name)
self.load_measurements(measurements_file_name)
self.workspace = cpw.Workspace(self.pipeline, self.module, None, None,
self.measurements, None)
self.module.module_num = len(self.pipeline.modules())+1
self.pipeline.add_module(self.module)
self.sizer = wx.BoxSizer(wx.VERTICAL)
module_panel = wx.lib.scrolledpanel.ScrolledPanel(self,-1,style=wx.SUNKEN_BORDER)
module_panel.BackgroundColour = cpprefs.get_background_color()
self.BackgroundColour = cpprefs.get_background_color()
self.module_view = ModuleView(module_panel, self.workspace, True)
self.module_view.set_selection(self.module.module_num)
def on_change(caller, event):
setting = event.get_setting()
proposed_value = event.get_proposed_value()
setting.value = proposed_value
self.pipeline.edit_module(event.get_module().module_num, False)
self.module_view.reset_view()
self.module_view.add_listener(on_change)
#
# Add a panel for the "run" button
#
panel = wx.Panel(self)
panel_sizer = wx.BoxSizer(wx.HORIZONTAL)
button = wx.Button(panel, label = "Run")
self.sizer.Add(module_panel, 1, wx.EXPAND)
self.sizer.Add(panel, 0, wx.EXPAND)
panel_sizer.AddStretchSpacer()
panel_sizer.Add(button, 0, wx.RIGHT, button.Size[1])
panel.SetSizer(panel_sizer)
wx.EVT_BUTTON(self, button.Id, self.on_run)
#
# Add a file menu
#
file_menu = wx.Menu()
file_menu.Append(ID_FILE_LOAD_MEASUREMENTS, "&Load measurements")
file_menu.Append(ID_FILE_SAVE_MEASUREMENTS, "&Save measurements")
file_menu.Append(ID_FILE_EXIT, "E&xit")
self.MenuBar = wx.MenuBar()
self.MenuBar.Append(file_menu, "&File")
self.Bind(wx.EVT_MENU, self.on_load_measurements, id=ID_FILE_LOAD_MEASUREMENTS)
self.Bind(wx.EVT_MENU, self.on_save_measurements, id=ID_FILE_SAVE_MEASUREMENTS)
self.Bind(wx.EVT_MENU, self.on_exit, id=ID_FILE_EXIT)
accelerators = wx.AcceleratorTable([
(wx.ACCEL_CMD, ord("W"), ID_FILE_EXIT),
(wx.ACCEL_CMD, ord("O"), ID_FILE_LOAD_MEASUREMENTS),
(wx.ACCEL_CMD, ord("S"), ID_FILE_SAVE_MEASUREMENTS)])
self.SetAcceleratorTable(accelerators)
#
# Add an image menu
#
image_menu = wx.Menu()
image_menu.Append(ID_IMAGE_CHOOSE, "&Choose")
self.MenuBar.Append(image_menu, "&Image")
self.Bind(wx.EVT_MENU, self.on_image_choose, id=ID_IMAGE_CHOOSE)
self.SetSizer(self.sizer)
self.Size = (self.module_view.get_max_width(), self.Size[1])
module_panel.Layout()
self.Show()
self.tbicon = wx.TaskBarIcon()
self.tbicon.SetIcon(get_cp_icon(), "CellProfiler2.0")
self.SetIcon(get_cp_icon())
def __init__(self, *args, **kwds):
'''Instantiate a data tool frame
module_name: name of module to instantiate
measurements_file_name: name of measurements file
'''
assert kwds.has_key(
"module_name"), "DataToolFrame() needs a module_name argument"
assert kwds.has_key(
"measurements_file_name"
), "DataToolFrame() needs a measurements_file_name argument"
module_name = kwds["module_name"]
measurements_file_name = kwds["measurements_file_name"]
kwds_copy = kwds.copy()
del kwds_copy["module_name"]
del kwds_copy["measurements_file_name"]
kwds_copy["title"] = "%s data tool" % module_name
wx.Frame.__init__(self, *args, **kwds_copy)
self.module = instantiate_module(module_name)
self.module.use_as_data_tool = True
self.pipeline = cpp.Pipeline()
if h5py.is_hdf5(measurements_file_name):
self.workspace = cpw.Workspace(self.pipeline, self.module, None,
None, None, None)
self.workspace.load(measurements_file_name, True)
self.measurements = self.workspace.measurements
else:
self.pipeline.load(measurements_file_name)
self.load_measurements(measurements_file_name)
self.workspace = cpw.Workspace(self.pipeline, self.module, None,
None, self.measurements, None)
self.module.module_num = len(self.pipeline.modules()) + 1
self.pipeline.add_module(self.module)
self.sizer = wx.BoxSizer(wx.VERTICAL)
module_panel = wx.lib.scrolledpanel.ScrolledPanel(
self, -1, style=wx.SUNKEN_BORDER)
module_panel.BackgroundColour = cpprefs.get_background_color()
self.BackgroundColour = cpprefs.get_background_color()
self.module_view = ModuleView(module_panel, self.workspace, True)
self.module_view.set_selection(self.module.module_num)
def on_change(caller, event):
setting = event.get_setting()
proposed_value = event.get_proposed_value()
setting.value = proposed_value
self.pipeline.edit_module(event.get_module().module_num, False)
self.module_view.reset_view()
self.module_view.request_validation()
self.module_view.add_listener(on_change)
#
# Add a panel for the "run" button
#
panel = wx.Panel(self)
panel_sizer = wx.BoxSizer(wx.HORIZONTAL)
button = wx.Button(panel, label="Run")
self.sizer.Add(module_panel, 1, wx.EXPAND)
self.sizer.Add(panel, 0, wx.EXPAND)
panel_sizer.AddStretchSpacer()
panel_sizer.Add(button, 0, wx.RIGHT, button.Size[1])
panel.SetSizer(panel_sizer)
wx.EVT_BUTTON(self, button.Id, self.on_run)
#
# Add a file menu
#
file_menu = wx.Menu()
file_menu.Append(ID_FILE_LOAD_MEASUREMENTS, "&Load measurements")
file_menu.Append(ID_FILE_SAVE_MEASUREMENTS, "&Save measurements")
file_menu.Append(ID_FILE_EXIT, "E&xit")
self.MenuBar = wx.MenuBar()
self.MenuBar.Append(file_menu, "&File")
self.Bind(wx.EVT_MENU,
self.on_load_measurements,
id=ID_FILE_LOAD_MEASUREMENTS)
self.Bind(wx.EVT_MENU,
self.on_save_measurements,
id=ID_FILE_SAVE_MEASUREMENTS)
self.Bind(wx.EVT_MENU, self.on_exit, id=ID_FILE_EXIT)
accelerators = wx.AcceleratorTable([
(wx.ACCEL_CMD, ord("W"), ID_FILE_EXIT),
(wx.ACCEL_CMD, ord("O"), ID_FILE_LOAD_MEASUREMENTS),
(wx.ACCEL_CMD, ord("S"), ID_FILE_SAVE_MEASUREMENTS)
])
self.SetAcceleratorTable(accelerators)
#
# Add an image menu
#
image_menu = wx.Menu()
image_menu.Append(ID_IMAGE_CHOOSE, "&Choose")
self.MenuBar.Append(image_menu, "&Image")
self.Bind(wx.EVT_MENU, self.on_image_choose, id=ID_IMAGE_CHOOSE)
self.SetSizer(self.sizer)
self.Size = (self.module_view.get_max_width(), self.Size[1])
module_panel.Layout()
self.Show()
self.tbicon = wx.TaskBarIcon()
self.tbicon.SetIcon(get_cp_icon(), "CellProfiler2.0")
self.SetIcon(get_cp_icon())
def test_00_00_instantiate(self):
instantiate_module(MODULE_NAME)
def make_instance(self):
'''Return an instance of example1 this way because it's not on classpath'''
return instantiate_module("Example1a")
def test_01_01_instantiate(self):
try:
instantiate_module(MODULE_NAME)
except:
self.fail("CellProfiler could not create your module. "
"Is it named, " + MODULE_NAME + "?")
def make_instance(self):
'''Return an instance of of the module'''
return instantiate_module("BayesianOptimisation")
def test_01_02_run(self):
module = instantiate_module(MODULE_NAME)
module.input_objects_name.value = INPUT_OBJECTS_NAME
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
module.module_num = 1
pipeline = cpp.Pipeline()
pipeline.add_module(module)
object_set = cpo.ObjectSet()
#
# Pick a bunch of random points, dilate them using the distance
# transform and then label the result.
#
r = np.random.RandomState()
r.seed(12)
bimg = np.ones((100, 100), bool)
bimg[r.randint(0,100, 50), r.randint(0, 100, 50)] = False
labels, count = label(distance_transform_edt(bimg) <= 5)
#
# Make the input objects
#
input_objects = cpo.Objects()
input_objects.segmented = labels
expected = skeletonize_labels(labels)
object_set.add_objects(input_objects, INPUT_OBJECTS_NAME)
#
# Make the workspace
#
measurements = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module, None, object_set,
measurements, None)
module.run(workspace)
#
# Calculate the centers using Numpy. Scipy can do this too.
# But maybe it's instructive to show you how to go at the labels
# matrix using Numpy.
#
# We're going to get the centroids by taking the average value
# of x and y per object.
#
y, x = np.mgrid[0:labels.shape[0], 0:labels.shape[1]].astype(float)
#
# np.bincount counts the number of occurrences of each integer value.
# You need to operate on a 1d array - if you flatten the labels
# and weights, their pixels still align.
#
# We do [1:] to discard the background which is labeled 0
#
# The optional second argument to np.bincount is the "weight". For
# each label value, maintain a running sum of the weights.
#
areas = np.bincount(expected.flatten())[1:]
total_x = np.bincount(expected.flatten(), weights=x.flatten())[1:]
total_y = np.bincount(expected.flatten(), weights=y.flatten())[1:]
expected_location_x = total_x / areas
expected_location_y = total_y / areas
#
# Now check against the measurements.
#
count_feature = I.C_COUNT + "_" + OUTPUT_OBJECTS_NAME
self.assertTrue(measurements.has_feature(cpmeas.IMAGE, count_feature),
"Your module did not produce a %s measurement" %
count_feature)
count = measurements.get_measurement(cpmeas.IMAGE, count_feature)
self.assertEqual(count, len(areas))
for ftr, expected in ((I.M_LOCATION_CENTER_X, expected_location_x),
(I.M_LOCATION_CENTER_Y, expected_location_y)):
self.assertTrue(measurements.has_feature(
OUTPUT_OBJECTS_NAME, ftr))
location = measurements.get_measurement(OUTPUT_OBJECTS_NAME, ftr)
np.testing.assert_almost_equal(location, expected)
def setUp(self):
#
# Get the module and class using CellProfiler's loader
#
self.module = instantiate_module("Example1f")
self.E = __import__(self.module.__class__.__module__)
def make_instance(self):
'''Return an instance of of the module'''
return instantiate_module("ManualEvaluation")
def test_01_01_output_module_html(self):
from cellprofiler.modules import get_module_names, instantiate_module
M.output_module_html(self.temp_dir)
for module_name in sorted(get_module_names()):
fd = None
try:
fd = open(os.path.join(self.temp_dir, module_name + ".html"))
except:
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
traceback.print_exc()
self.assert_("Failed to open %s.html" % module_name)
data = fd.read()
fd.close()
#
# Make sure that some nesting rules are obeyed.
#
tags_we_care_about = ("i", "b", "ul", "ol", "li", "table", "tr",
"td", "th", "h1", "h2", "h3", "html", "head",
"body")
pattern = r"<\s*([a-zA-Z0-9]+).[^>]*>"
anti_pattern = r"</\s*([a-zA-Z0-9]+)[^>]*>"
d = {}
anti_d = {}
COUNT = 0
LIST = 1
for tag in tags_we_care_about:
for dd in (d, anti_d):
dd[tag] = [0, []]
for p, dd in ((pattern, d), (anti_pattern, anti_d)):
pos = 0
while (True):
m = re.search(p, data[pos:])
if m is None:
break
tag = m.groups()[0].lower()
pos = pos + m.start(1) + 1
if dd.has_key(tag):
dd[tag][COUNT] += 1
dd[tag][LIST].append(pos)
#
# Check table nesting rules
#
T_TABLE = 0
T_ANTI_TABLE = 1
T_TR = 2
T_ANTI_TR = 3
T_TH = 4
T_ANTI_TH = 5
T_TD = 6
T_ANTI_TD = 7
T_UL = 8
T_ANTI_UL = 9
T_OL = 10
T_ANTI_OL = 11
T_LI = 12
T_ANTI_LI = 13
T_I = 14
T_ANTI_I = 15
T_B = 16
T_ANTI_B = 17
tokens = []
for tag, token, anti_token in (('table', T_TABLE, T_ANTI_TABLE),
('tr', T_TR, T_ANTI_TR),
('td', T_TD, T_ANTI_TD),
('th', T_TH,
T_ANTI_TH), ('ul', T_UL,
T_ANTI_UL),
('ol', T_OL,
T_ANTI_OL), ('li', T_LI,
T_ANTI_LI),
('i', T_I, T_ANTI_I), ('b', T_B,
T_ANTI_B)):
tokens += [(pos, token) for pos in d[tag][LIST]]
tokens += [(pos, anti_token) for pos in anti_d[tag][LIST]]
tokens = sorted(tokens)
S_INIT = 0
S_AFTER_TABLE = 1
S_AFTER_TR = 2
S_AFTER_TD = 3
S_AFTER_TH = 4
S_AFTER_OL = 5
S_AFTER_UL = 6
S_AFTER_LI = 7
S_AFTER_I = 8
S_AFTER_B = 9
state_transitions = {
S_INIT: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_I: S_AFTER_I,
T_B: S_AFTER_B
},
S_AFTER_TABLE: {
T_ANTI_TABLE: S_INIT,
T_TR: S_AFTER_TR
},
S_AFTER_TR: {
T_ANTI_TR: S_INIT,
T_TD: S_AFTER_TD,
T_TH: S_AFTER_TH
},
S_AFTER_TD: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_ANTI_TD: S_INIT
},
S_AFTER_TH: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_ANTI_TH: S_INIT
},
S_AFTER_OL: {
T_LI: S_AFTER_LI,
T_ANTI_OL: S_INIT
},
S_AFTER_UL: {
T_LI: S_AFTER_LI,
T_ANTI_UL: S_INIT
},
S_AFTER_LI: {
T_ANTI_LI: S_INIT,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I
},
S_AFTER_I: {
T_ANTI_I: S_INIT,
T_I: S_AFTER_I, # Stupid but legal <i><i>Foo</i></i>
T_B: S_AFTER_B,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL
},
S_AFTER_B: {
T_ANTI_B: S_INIT,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL
}
}
state = []
for pos, token in tokens:
self.assertTrue(
len(state) >= 0, "Error in %s near position %d (%s)" %
(module_name, pos,
data[max(0, pos - 30):max(pos + 30, len(data))]))
top_state, start_pos = (S_INIT,
0) if len(state) == 0 else state[-1]
self.assertTrue(
state_transitions[top_state].has_key(token),
"Nesting error in %s near position %d (%s)" %
(module_name, pos, data[max(0, pos - 50):pos] + "^^^" +
data[pos:min(pos + 50, len(data))]))
next_state = state_transitions[top_state][token]
if next_state == S_INIT:
state.pop()
else:
state.append((next_state, pos))
if len(state) > 0:
self.assertEqual(
len(state), 0,
"Couldn't find last closing tag in %s. Last tag position = %d (%s)"
% (module_name, state[-1][1],
data[(state[-1][1] - 30):(state[-1][1] + 30)]))
#
# Check begin/end tag counts
#
for tag in tags_we_care_about:
if d.has_key(tag):
self.assertTrue(
anti_d.has_key(tag),
"Missing closing </%s> tag in %s" % (tag, module_name))
self.assertEqual(
d[tag][COUNT], anti_d[tag][COUNT],
"Found %d <%s>, != %d </%s> in %s" %
(d[tag][COUNT], tag, anti_d[tag][COUNT], tag,
module_name))
else:
self.assertFalse(
anti_d.has_key(tag),
"Missing opening <%s> tag in %s" % (tag, module_name))
def test_01_02_run(self):
module = instantiate_module(MODULE_NAME)
module.input_objects_name.value = INPUT_OBJECTS_NAME
module.output_objects_name.value = OUTPUT_OBJECTS_NAME
module.module_num = 1
pipeline = cpp.Pipeline()
pipeline.add_module(module)
object_set = cpo.ObjectSet()
#
# Pick a bunch of random points, dilate them using the distance
# transform and then label the result.
#
r = np.random.RandomState()
r.seed(12)
bimg = np.ones((100, 100), bool)
bimg[r.randint(0, 100, 50), r.randint(0, 100, 50)] = False
labels, count = label(distance_transform_edt(bimg) <= 5)
#
# Make the input objects
#
input_objects = cpo.Objects()
input_objects.segmented = labels
expected = skeletonize_labels(labels)
object_set.add_objects(input_objects, INPUT_OBJECTS_NAME)
#
# Make the workspace
#
measurements = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module, None, object_set,
measurements, None)
module.run(workspace)
#
# Calculate the centers using Numpy. Scipy can do this too.
# But maybe it's instructive to show you how to go at the labels
# matrix using Numpy.
#
# We're going to get the centroids by taking the average value
# of x and y per object.
#
y, x = np.mgrid[0:labels.shape[0], 0:labels.shape[1]].astype(float)
#
# np.bincount counts the number of occurrences of each integer value.
# You need to operate on a 1d array - if you flatten the labels
# and weights, their pixels still align.
#
# We do [1:] to discard the background which is labeled 0
#
# The optional second argument to np.bincount is the "weight". For
# each label value, maintain a running sum of the weights.
#
areas = np.bincount(expected.flatten())[1:]
total_x = np.bincount(expected.flatten(), weights=x.flatten())[1:]
total_y = np.bincount(expected.flatten(), weights=y.flatten())[1:]
expected_location_x = total_x / areas
expected_location_y = total_y / areas
#
# Now check against the measurements.
#
count_feature = I.C_COUNT + "_" + OUTPUT_OBJECTS_NAME
self.assertTrue(
measurements.has_feature(cpmeas.IMAGE, count_feature),
"Your module did not produce a %s measurement" % count_feature)
count = measurements.get_measurement(cpmeas.IMAGE, count_feature)
self.assertEqual(count, len(areas))
for ftr, expected in ((I.M_LOCATION_CENTER_X, expected_location_x),
(I.M_LOCATION_CENTER_Y, expected_location_y)):
self.assertTrue(measurements.has_feature(OUTPUT_OBJECTS_NAME, ftr))
location = measurements.get_measurement(OUTPUT_OBJECTS_NAME, ftr)
np.testing.assert_almost_equal(location, expected)
def make_instance(self):
return instantiate_module("Example3a")
import cellprofiler.objects as cpo
import cellprofiler.measurements as cpm
import cellprofiler.pipeline as cpp
import cellprofiler.settings as cps
import cellprofiler.workspace as cpw
import cellprofiler.modules.run_imagej as R
import imagej.imagej2 as ij2
INPUT_IMAGE_NAME = "inputimage"
OUTPUT_IMAGE_NAME = "outputimage"
from cellprofiler.modules import instantiate_module
try:
instantiate_module("RunImageJ")
skip_tests = False
except:
skip_tests = True
@unittest.skipIf(skip_tests, "RunImageJ did not load (headless?)")
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
def search_module_help(text):
'''Search the help for a string
text - find text in the module help using case-insensitive matching
returns an html document of all the module help pages that matched or
None if no match found.
'''
matching_help = []
for item in MAIN_HELP:
matching_help += __search_menu_helper(
item, lambda x:__search_fn(x, text))
count = sum([len(x[2]) for x in matching_help])
for module_name in get_module_names():
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
help_text = module.get_help()
matches = __search_fn(help_text, text)
if len(matches) > 0:
matching_help.append((module_name, help_text, matches))
count += len(matches)
if len(matching_help) == 0:
return None
top = """<html style="font-family:arial">
<head><title>%s found</title></head>
<body><h1>Matches found</h1><br><ul>
""" % ("1 match" if len(matching_help) == 1 else "%d matches" % len(matching_help))
body = "<br>"
match_num = 1
prev_link = (
'<a href="#match%d" title="Previous match">'
'<img src="memory:previous.png" alt="previous match"></a>')
anchor = '<a name="match%d"><u>%s</u></a>'
next_link = ('<a href="#match%d" title="Next match">'
'<img src="memory:next.png" alt="next match"></a>')
for title, help_text, pairs in matching_help:
top += """<li><a href="#match%d">%s</a></li>\n""" % (
match_num, title)
if help_text.find("<h1>") == -1:
body += "<h1>%s</h1>" % title
start_match = re.search(r"<\s*body[^>]*?>", help_text, re.IGNORECASE)
if start_match is None:
start = 0
else:
start = start_match.end()
end_match = re.search(r"<\\\s*body", help_text, re.IGNORECASE)
if end_match is None:
end = len(help_text)
else:
end = end_match.start()
for begin_pos, end_pos in pairs:
body += help_text[start:begin_pos]
if match_num > 1:
body += prev_link % (match_num - 1)
body += anchor % (match_num, help_text[begin_pos:end_pos])
if match_num != count:
body += next_link % (match_num + 1)
start = end_pos
match_num += 1
body += help_text[start:end] + "<br>"
result = "%s</ul><br>\n%s</body></html>" % (top, body)
return result
def setUp(self):
#
# Get the module and class using CellProfiler's loader
#
self.module = instantiate_module("Example1f")
self.E = __import__(self.module.__class__.__module__)
def setUp(self):
self.module = instantiate_module("Example3b")
self.module.input_image_name.value = INPUT_IMAGE_NAME
self.E = __import__(self.module.__class__.__module__)
def setUp(self):
self.module = instantiate_module("Example3b")
self.module.input_image_name.value = INPUT_IMAGE_NAME
self.E = __import__(self.module.__class__.__module__)
