def test_plot_profile(self):
script_id = super(TestAnalysisScripts, self).get_script(plot_profile)
assert script_id > 0
client, user = self.new_client_and_user()
# create a test image
size_t = 3
size_x = 100
size_y = 100
session = client.getSession()
image = self.create_test_image(size_x, size_y, 1, 2, size_t, session)
image_id = image.id.val
roi = create_roi(image_id, 0, size_x / 2, 0, size_y / 2, size_t, True)
session.getUpdateService().saveAndReturnObject(roi)
image_ids = []
image_ids.append(omero.rtypes.rlong(image_id))
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids),
"Line_Width": omero.rtypes.rint(2),
"Sum_or_Average": omero.rtypes.rstring("Average")
}
ann = run_script(client, script_id, args, "Line_Data")
c = self.new_client(user=user)
check_file_annotation(c, ann)
def test_movie_figure(self, all_parameters):
sid = super(TestFigureExportScripts, self).get_script(movie_figure)
assert sid > 0
client, user = self.new_client_and_user()
# create several test images in a dataset
dataset = self.make_dataset("movieFig-test", client=client)
project = self.make_project("movieFig-test", client=client)
self.link(project, dataset, client=client)
# put some images in dataset
session = client.getSession()
image_ids = []
for i in range(2):
image = self.create_test_image(256, 256, 5, 3, 20, session)
image_ids.append(omero.rtypes.rlong(image.id.val))
self.link(dataset, image, client=client)
red = omero.rtypes.rint(16711680)
t_indexes = [
omero.rtypes.rint(0),
omero.rtypes.rint(1),
omero.rtypes.rint(5),
omero.rtypes.rint(10),
omero.rtypes.rint(15)
]
if all_parameters:
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids),
"T_Indexes": omero.rtypes.rlist(t_indexes),
"Z_Start": omero.rtypes.rint(1),
"Z_End": omero.rtypes.rint(3),
"Width": omero.rtypes.rint(150),
"Height": omero.rtypes.rint(150),
"Image_Labels": omero.rtypes.rstring("Datasets"),
"Algorithm": omero.rtypes.rstring("Mean Intensity"),
"Stepping": omero.rtypes.rint(1),
"Scalebar": omero.rtypes.rint(10),
"Format": omero.rtypes.rstring("PNG"),
"Figure_Name": omero.rtypes.rstring("movieFigureTest"),
"TimeUnits": omero.rtypes.rstring("MINS"),
"Overlay_Colour": red,
}
else:
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids),
"T_Indexes": omero.rtypes.rlist(t_indexes)
}
ann = run_script(client, sid, args, "File_Annotation")
c = self.new_client(user=user)
check_file_annotation(c, ann)
def test_thumbnail_figure(self, data_type, all_parameters):
sid = super(TestFigureExportScripts, self).get_script(thumbnail_figure)
assert sid > 0
client, user = self.new_client_and_user()
# create several test images in a dataset
dataset = self.make_dataset("thumbnailFigure-test", client=client)
# make some tags
tag_ids = []
session = client.getSession()
for t in range(5):
tag = omero.model.TagAnnotationI()
tag.setTextValue(omero.rtypes.rstring("TestTag_%s" % t))
tag = session.getUpdateService().saveAndReturnObject(tag)
tag_ids.append(tag.id)
# put some images in dataset
image_ids = []
for i in range(2):
# x,y,z,c,t
image = self.create_test_image(100, 100, 1, 1, 1, session)
image_ids.append(omero.rtypes.rlong(image.id.val))
self.link(dataset, image, client=client)
# add tag
t = i % 5
tag = omero.model.TagAnnotationI(tag_ids[t].val, False)
self.link(image, tag, client=client)
dataset_ids = [omero.rtypes.rlong(dataset.id.val)]
ids = image_ids
if data_type == "Dataset":
ids = dataset_ids
if all_parameters:
args = {
"IDs": omero.rtypes.rlist(ids),
"Data_Type": omero.rtypes.rstring(data_type),
"Thumbnail_Size": omero.rtypes.rint(16),
"Max_Columns": omero.rtypes.rint(6),
"Format": omero.rtypes.rstring("PNG"),
"Figure_Name": omero.rtypes.rstring("thumbnail-test"),
"Tag_IDs": omero.rtypes.rlist(tag_ids)
}
else:
args = {
"Data_Type": omero.rtypes.rstring(data_type),
"IDs": omero.rtypes.rlist(ids)
}
ann = run_script(client, sid, args, "File_Annotation")
# should have figures attached to dataset and first image.
c = self.new_client(user=user)
check_file_annotation(c, ann, parent_type=data_type)
def test_movie_roi_figure(self, all_parameters):
sid = super(TestFigureExportScripts, self).get_script(movie_roi_figure)
assert sid > 0
client, user = self.new_client_and_user()
# create several test images in a dataset
dataset = self.make_dataset("movieRoiFig-test", client=client)
project = self.make_project("movieRoiFig-test", client=client)
self.link(project, dataset, client=client)
# put some images in dataset
image_ids = []
session = client.getSession()
for i in range(2):
image = self.create_test_image(256, 256, 10, 3, 1, session)
image_ids.append(omero.rtypes.rlong(image.id.val))
self.link(dataset, image, client=client)
# add roi - x, y, width, height
add_rectangle_roi(session.getUpdateService(), 50 + (i * 10),
100 - (i * 10), 50 + (i * 5), 100 - (i * 5),
image.id.val)
if all_parameters:
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids),
"ROI_Zoom": omero.rtypes.rfloat(3),
"Max_Columns": omero.rtypes.rint(10),
"Resize_Images": omero.rtypes.rbool(True),
"Width": omero.rtypes.rint(200),
"Height": omero.rtypes.rint(200),
"Image_Labels": omero.rtypes.rstring("Datasets"),
"Show_ROI_Duration": omero.rtypes.rbool(True),
# will be ignored since no pixelsize set
"Scalebar": omero.rtypes.rint(10),
# will be ignored since no pixelsize set
"Scalebar_Colour": omero.rtypes.rstring("White"),
# won't be found - but should still work
"Roi_Selection_Label": omero.rtypes.rstring("fakeTest"),
"Algorithm": omero.rtypes.rstring("Mean Intensity"),
"Figure_Name": omero.rtypes.rstring("movieROITest")
}
else:
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids)
}
ann = run_script(client, sid, args, "File_Annotation")
c = self.new_client(user=user)
check_file_annotation(c, ann)
def test_batch_image_export(self):
sid = super(TestExportScripts, self).get_script(batch_image_export)
assert sid > 0
client, user = self.new_client_and_user()
# x,y,z,c,t
image = self.create_test_image(100, 100, 1, 1, 1, client.getSession())
image_ids = []
image_ids.append(rlong(image.id.val))
args = {"Data_Type": rstring("Image"), "IDs": rlist(image_ids)}
ann = run_script(client, sid, args, "File_Annotation")
c = self.new_client(user=user)
check_file_annotation(c, ann)
def test_export_figure_as(self, export_option, tmpdir):
"""Create images, add to figure and export as TIFF, PNG etc."""
id = super(TestFigureScripts, self).get_script_by_name(path, name)
assert id > 0
# client, user = self.new_client_and_user()
# Temp workaround for openmicroscopy/openmicroscopy/pull/5720
client = self.client
user = self.user
script_service = client.sf.getScriptService()
assert script_service.getParams(id) is not None
# create an image
size_t = 1
size_x = 100
size_y = 100
size_z = 1
size_c = 1
session = client.getSession()
image = self.create_test_image(size_x, size_y, size_z, size_c, size_t,
session)
image_id = self.import_pyramid(tmpdir, client=client)
query_service = client.sf.getQueryService()
big_image = query_service.findByQuery(
"""select i from Image i left outer join fetch i.pixels as p
where i.id = :id""",
ParametersI().addId(image_id))
figure_name = "test_export_figure_as_%s" % export_option
json = create_figure([image, big_image])
uri = "https://www.openmicroscopy.org/"
args = {
"Figure_JSON": omero.rtypes.rstring(json),
"Export_Option": omero.rtypes.rstring(export_option),
"Figure_Name": omero.rtypes.rstring(figure_name),
"Webclient_URI": omero.rtypes.rstring(uri)
}
robj = run_script(client, id, args, "New_Figure")
ann = robj.getValue()
# New image is returned when it is an OMERO image
if export_option is "OMERO":
assert isinstance(ann, Image)
else:
c = self.new_client(user=user)
check_file_annotation(c, ann, link_count=2)
def test_export_figure_as(self, export_option, tmpdir):
"""Create images, add to figure and export as TIFF, PNG etc."""
id = super(TestFigureScripts, self).get_script_by_name(path, name)
assert id > 0
# client, user = self.new_client_and_user()
# Temp workaround for openmicroscopy/openmicroscopy/pull/5720
client = self.client
user = self.user
script_service = client.sf.getScriptService()
assert script_service.getParams(id) is not None
# create an image
size_t = 1
size_x = 100
size_y = 100
size_z = 1
size_c = 1
session = client.getSession()
image = self.create_test_image(size_x, size_y, size_z, size_c,
size_t, session)
image_id = self.import_pyramid(tmpdir, client=client)
query_service = client.sf.getQueryService()
big_image = query_service.findByQuery(
"""select i from Image i left outer join fetch i.pixels as p
where i.id = :id""",
ParametersI().addId(image_id))
figure_name = "test_export_figure_as_%s" % export_option
json = create_figure([image, big_image])
uri = "https://www.openmicroscopy.org/"
args = {
"Figure_JSON": omero.rtypes.rstring(json),
"Export_Option": omero.rtypes.rstring(export_option),
"Figure_Name": omero.rtypes.rstring(figure_name),
"Webclient_URI": omero.rtypes.rstring(uri)
}
robj = run_script(client, id, args, "New_Figure")
ann = robj.getValue()
# New image is returned when it is an OMERO image
if export_option is "OMERO":
assert isinstance(ann, Image)
else:
c = self.new_client(user=user)
check_file_annotation(c, ann, link_count=2)
def test_kymograph_analysis(self):
script_id = super(TestAnalysisScripts, self).get_script(kymograph)
client, user = self.new_client_and_user()
# create a test image
size_t = 3
size_x = 100
size_y = 100
# x,y,z,c,t
session = client.getSession()
image = self.create_test_image(size_x, size_y, 1, 2, size_t, session)
image_id = image.id.val
roi = create_roi(image_id, 0, size_x / 2, 0, size_y / 2, size_t, True)
session.getUpdateService().saveAndReturnObject(roi)
image_ids = []
image_ids.append(omero.rtypes.rlong(image_id))
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids),
"Line_Width": omero.rtypes.rint(5)
}
kymograph_img = run_script(client, script_id, args, "New_Image")
# now analyse the Kymograph image
sid = super(TestAnalysisScripts, self).get_script(kymograph_analysis)
assert sid > 0
image_id = kymograph_img.getValue().id.val
roi = create_roi(image_id, 0, 2, 0, 2, 1, False)
session.getUpdateService().saveAndReturnObject(roi)
image_ids = []
image_ids.append(omero.rtypes.rlong(image_id))
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids)
}
ann = run_script(client, sid, args, "Line_Data")
c = self.new_client(user=user)
check_file_annotation(c, ann)
def test_batch_roi_export(self, all_planes):
sid = super(TestExportScripts, self).get_script(batch_roi_export)
assert sid > 0
client, user = self.new_client_and_user()
session = client.getSession()
# x,y,z,c,t
size_c = 2
size_z = 3
size_t = 4
image_name = "ROI_image"
label_text = "Shape_Text"
image = self.create_test_image(100,
100,
size_z,
size_c,
size_t,
session,
name=image_name)
# Add 2 Shapes... A Rectangle and Polygon covering same area
polygon = omero.model.PolygonI()
polygon.points = rstring("10,10, 91,10, 91,91, 10,91")
polygon.textValue = rstring(label_text)
rect = omero.model.RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(10)
rect.width = rdouble(81)
rect.height = rdouble(81)
rect.theZ = rint(1)
rect.theT = rint(1)
# ...to an ROI
roi = omero.model.RoiI()
roi.setImage(image)
roi.addShape(polygon)
roi.addShape(rect)
roi = session.getUpdateService().saveAndReturnObject(roi)
shapes = roi.copyShapes()
polygon = shapes[0]
image_ids = []
file_name = "test_batch_roi_export"
image_ids.append(rlong(image.id.val))
channels = [rint(c) for c in range(4)]
args = {
"Data_Type": rstring("Image"),
"IDs": rlist(image_ids),
# Should ignore Channels out of range. 1-based index
"Channels": rlist(channels),
"Export_All_Planes": rbool(all_planes),
"File_Name": rstring(file_name)
}
ann = run_script(client, sid, args, "File_Annotation")
c = self.new_client(user=user)
check_file_annotation(c, ann, file_name="%s.csv" % file_name)
file_id = ann.getValue().getFile().id.val
csv_text = get_file_contents(self.new_client(user=user), file_id)
# Check we have expected number of rows
polygon_planes = size_c
if all_planes:
polygon_planes = size_c * size_z * size_t
# Rows: Header + rect with Z/T set + polygon without Z/T
row_count = 1 + size_c + polygon_planes
assert len(csv_text.split("\n")) == row_count
# Check first 2 rows of csv (except Std dev)
zt = ","
points_min_max_sum_mean = ",,,,"
area = "6561.0"
if all_planes:
zt = "1,1"
points_min_max_sum_mean = "6561,10.0,90.0,328050.0,50.0"
expected = ("image_id,image_name,roi_id,shape_id,type,text,"
"z,t,channel,area (pixels),length (pixels),"
"points,min,max,sum,mean,std_dev,"
"X,Y,Width,Height,RadiusX,RadiusY,X1,Y1,X2,Y2,Points\n"
"%s,\"%s\",%s,%s,polygon,\"%s\",%s,0,%s,,%s,") % (
image.id.val, image_name, roi.id.val, polygon.id.val,
label_text, zt, area, points_min_max_sum_mean)
assert csv_text.startswith(expected)
def test_split_view_figure(self, all_parameters):
id = super(TestFigureExportScripts, self).get_script(split_view_figure)
assert id > 0
client, user = self.new_client_and_user()
# create several test images in a dataset
dataset = self.make_dataset("thumbnailFigure-test", client=client)
project = self.make_project("thumbnailFigure-test", client=client)
self.link(project, dataset, client=client)
# put some images in dataset
session = client.getSession()
image_ids = []
for i in range(2):
image = self.create_test_image(256, 200, 5, 4, 1, session)
image_ids.append(omero.rtypes.rlong(image.id.val))
self.link(dataset, image, client=client)
c_names_map = omero.rtypes.rmap({
'0': omero.rtypes.rstring("DAPI"),
'1': omero.rtypes.rstring("GFP"),
'2': omero.rtypes.rstring("Red"),
'3': omero.rtypes.rstring("ACA")
})
blue = omero.rtypes.rlong(255)
red = omero.rtypes.rlong(16711680)
mrgd_colours_map = omero.rtypes.rmap({'0': blue, '1': blue, '3': red})
if all_parameters:
args = {
"Data_Type":
omero.rtypes.rstring("Image"),
"IDs":
omero.rtypes.rlist(image_ids),
"Z_Start":
omero.rtypes.rint(0),
"Z_End":
omero.rtypes.rint(3),
"Channel_Names":
c_names_map,
"Split_Indexes":
omero.rtypes.rlist(
[omero.rtypes.rint(1),
omero.rtypes.rint(2)]),
"Split_Panels_Grey":
omero.rtypes.rbool(True),
"Merged_Colours":
mrgd_colours_map,
"Merged_Names":
omero.rtypes.rbool(True),
"Width":
omero.rtypes.rint(200),
"Height":
omero.rtypes.rint(200),
"Image_Labels":
omero.rtypes.rstring("Datasets"),
"Algorithm":
omero.rtypes.rstring("Mean Intensity"),
"Stepping":
omero.rtypes.rint(1),
# will be ignored since no pixelsize set
"Scalebar":
omero.rtypes.rint(10),
"Format":
omero.rtypes.rstring("PNG"),
"Figure_Name":
omero.rtypes.rstring("splitViewTest"),
}
else:
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids),
"Merged_Colours": mrgd_colours_map,
"Format": omero.rtypes.rstring("PNG"),
"Figure_Name": omero.rtypes.rstring("splitViewTest")
}
ann = run_script(client, id, args, "File_Annotation")
c = self.new_client(user=user)
check_file_annotation(c, ann)
def test_roi_figure(self, all_parameters):
sid = super(TestFigureExportScripts, self).get_script(roi_figure)
assert sid > 0
client, user = self.new_client_and_user()
# create several test images in a dataset
dataset = self.make_dataset("roiFig-test", client=client)
project = self.make_project("roiFig-test", client=client)
self.link(project, dataset, client=client)
# put some images in dataset
image_ids = []
session = client.getSession()
for i in range(2):
image = self.create_test_image(256, 200, 5, 4, 1, session)
image_ids.append(omero.rtypes.rlong(image.id.val))
self.link(dataset, image, client=client)
add_rectangle_roi(session.getUpdateService(), 50 + (i * 10),
100 - (i * 10), 50 + (i * 5), 100 - (i * 5),
image.id.val)
c_names_map = omero.rtypes.rmap({
'0': omero.rtypes.rstring("DAPI"),
'1': omero.rtypes.rstring("GFP"),
'2': omero.rtypes.rstring("Red"),
'3': omero.rtypes.rstring("ACA")
})
blue = omero.rtypes.rint(255)
red = omero.rtypes.rint(16711680)
mrgd_colours_map = omero.rtypes.rmap({'0': blue, '1': blue, '3': red})
if all_parameters:
args = {
"Data_Type":
omero.rtypes.rstring("Image"),
"IDs":
omero.rtypes.rlist(image_ids),
"Channel_Names":
c_names_map,
"Split_Indexes":
omero.rtypes.rlist(
[omero.rtypes.rlong(1),
omero.rtypes.rlong(2)]),
"Split_Panels_Grey":
omero.rtypes.rbool(True),
"Merged_Colours":
mrgd_colours_map,
"Merged_Names":
omero.rtypes.rbool(True),
"Width":
omero.rtypes.rint(200),
"Height":
omero.rtypes.rint(200),
"Image_Labels":
omero.rtypes.rstring("Datasets"),
"Algorithm":
omero.rtypes.rstring("Mean Intensity"),
"Stepping":
omero.rtypes.rint(1),
# will be ignored since no pixelsize set
"Scalebar":
omero.rtypes.rint(10),
"Format":
omero.rtypes.rstring("PNG"),
"Figure_Name":
omero.rtypes.rstring("splitViewTest"),
"Overlay_Colour":
omero.rtypes.rstring("Red"),
"ROI_Zoom":
omero.rtypes.rfloat(3),
# won't be found - but should still work
"ROI_Label":
omero.rtypes.rstring("fakeTest"),
}
else:
args = {
"Data_Type": omero.rtypes.rstring("Image"),
"IDs": omero.rtypes.rlist(image_ids)
}
ann = run_script(client, sid, args, "File_Annotation")
c = self.new_client(user=user)
check_file_annotation(c, ann)
