def run_script():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
data_types = [rstring('Image')]
labels = [rstring('Image Name'), rstring('Datasets'), rstring('Tags')]
algorithms = [rstring('Maximum Intensity'), rstring('Mean Intensity')]
formats = [rstring('JPEG'), rstring('PNG'), rstring('TIFF')]
ckeys = COLOURS.keys()
ckeys.sort()
o_colours = wrap(OVERLAY_COLOURS.keys())
client = scripts.client(
'Split_View_Figure.py',
"""Create a figure of split-view images.
See http://help.openmicroscopy.org/publish.html#figures""",
# provide 'Data_Type' and 'IDs' parameters so that Insight
# auto-populates with currently selected images.
scripts.String("Data_Type",
optional=False,
grouping="01",
description="The data you want to work with.",
values=data_types,
default="Image"),
scripts.List("IDs",
optional=False,
grouping="02",
description="List of Image IDs").ofType(rlong(0)),
scripts.String(
"Algorithm",
grouping="3",
description="Algorithm for projection. Only used if a Z-range is"
" chosen below",
values=algorithms,
default='Maximum Intensity'),
scripts.Int(
"Z_Start",
grouping="3.1",
description="Projection range (if not specified, use defaultZ"
" only - no projection)",
min=0),
scripts.Int(
"Z_End",
grouping="3.2",
description="Projection range (if not specified, use defaultZ"
" only - no projection)",
min=0),
scripts.Map("Channel_Names",
grouping="4",
description="Map of index: channel name for all channels"),
scripts.List("Split_Indexes",
grouping="5",
description="List of the channels in the split"
" view").ofType(rint(0)),
scripts.Bool("Split_Panels_Grey",
grouping="6",
description="If true, all split panels are grayscale",
default=False),
scripts.Map(
"Merged_Colours",
grouping="7",
description="Map of index:int colors for each merged channel"),
scripts.Bool(
"Merged_Names",
grouping="8",
description="If true, label the merged panel with channel names."
" Otherwise label with 'Merged'",
default=True),
scripts.Int("Width",
grouping="9",
description="The max width of each image panel. Default is"
" first image width",
min=1),
scripts.Int(
"Height",
grouping="91",
description="The max height of each image panel. Default is"
" first image height",
min=1),
scripts.String(
"Image_Labels",
grouping="92",
description="Label images with Image name (default) or datasets"
" or tags",
values=labels,
default='Image Name'),
scripts.Int("Stepping",
grouping="93",
description="The Z increment for projection.",
default=1,
min=1),
scripts.Int(
"Scalebar",
grouping="94",
description="Scale bar size in microns. Only shown if image has"
" pixel-size info.",
min=1),
scripts.String("Format",
grouping="95",
description="Format to save image",
values=formats,
default='JPEG'),
scripts.String("Figure_Name",
grouping="96",
description="File name of the figure to save.",
default='Split_View_Figure'),
scripts.String("Overlay_Colour",
grouping="97",
description="The color of the scale bar.",
default='White',
values=o_colours),
version="4.3.0",
authors=["William Moore", "OME Team"],
institutions=["University of Dundee"],
contact="*****@*****.**",
)
try:
conn = BlitzGateway(client_obj=client)
script_params = client.getInputs(unwrap=True)
# call the main script, attaching resulting figure to Image. Returns
# the FileAnnotationI
[file_annotation, message] = split_view_figure(conn, script_params)
# Return message and file annotation (if applicable) to the client
client.setOutput("Message", rstring(message))
if file_annotation is not None:
client.setOutput("File_Annotation", robject(file_annotation._obj))
finally:
client.closeSession()
def runAsScript():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
dataTypes = [rstring('Image')]
labels = [rstring('Image Name'), rstring('Datasets'), rstring('Tags')]
algorithums = [rstring('Maximum Intensity'), rstring('Mean Intensity')]
roiLabel = """Specify an ROI to pick by specifying it's shape label. \
'FigureROI' by default, (not case sensitive). If matching ROI not found, use \
any ROI."""
formats = [rstring('JPEG'), rstring('PNG'), rstring('TIFF')]
ckeys = COLOURS.keys()
ckeys.sort()
oColours = wrap(OVERLAY_COLOURS.keys())
client = scripts.client(
'ROI_Split_Figure.py',
"""Create a figure of an ROI region as separate zoomed split-channel \
panels.
NB: OMERO.insight client provides a nicer UI for this script under \
'Publishing Options'
See http://help.openmicroscopy.org/scripts.html""",
# provide 'Data_Type' and 'IDs' parameters so that Insight
# auto-populates with currently selected images.
scripts.String(
"Data_Type", optional=False, grouping="01",
description="The data you want to work with.",
values=dataTypes, default="Image"),
scripts.List(
"IDs", optional=False, grouping="02",
description="List of Dataset IDs or Image IDs").ofType(rlong(0)),
scripts.Map(
"Channel_Names", grouping="03",
description="Map of index: channel name for All channels"),
scripts.Bool(
"Merged_Names", grouping="04",
description="If true, label the merged panel with channel names."
" Otherwise label with 'Merged'"),
scripts.List(
"Split_Indexes", grouping="05",
description="List of the channels in the split view panels"),
scripts.Bool(
"Split_Panels_Grey", grouping="06",
description="If true, all split panels are grayscale"),
scripts.Map(
"Merged_Colours", grouping="07",
description="Map of index:int colors for each merged channel."
" Otherwise use existing colour settings"),
scripts.Int(
"Width", grouping="08",
description="Max width of each image panel", min=1),
scripts.Int(
"Height", grouping="09",
description="The max height of each image panel", min=1),
scripts.String(
"Image_Labels", grouping="10",
description="Label images with the Image's Name or it's Datasets"
" or Tags", values=labels),
scripts.String(
"Algorithm", grouping="11",
description="Algorithum for projection.", values=algorithums),
scripts.Int(
"Stepping", grouping="12",
description="The Z-plane increment for projection. Default is 1",
min=1),
scripts.Int(
"Scalebar", grouping="13",
description="Scale bar size in microns. Only shown if image has"
" pixel-size info.", min=1),
scripts.String(
"Format", grouping="14",
description="Format to save image. E.g 'PNG'.",
values=formats, default='JPEG'),
scripts.String(
"Figure_Name", grouping="15",
description="File name of the figure to save."),
scripts.String(
"Overlay_Colour", grouping="16",
description="The color of the scale bar.",
default='White', values=oColours),
scripts.Float(
"ROI_Zoom", grouping="17",
description="How much to zoom the ROI. E.g. x 2. If 0 then zoom"
" roi panel to fit", min=0),
scripts.String("ROI_Label", grouping="18", description=roiLabel),
version="4.3.0",
authors=["William Moore", "OME Team"],
institutions=["University of Dundee"],
contact="*****@*****.**",
)
try:
conn = BlitzGateway(client_obj=client)
commandArgs = client.getInputs(unwrap=True)
print commandArgs
# call the main script, attaching resulting figure to Image. Returns
# the id of the originalFileLink child. (ID object, not value)
fileAnnotation, message = roiFigure(conn, commandArgs)
# Return message and file annotation (if applicable) to the client
client.setOutput("Message", rstring(message))
if fileAnnotation is not None:
client.setOutput("File_Annotation", robject(fileAnnotation._obj))
finally:
client.closeSession()
def runAsScript():
"""
The main entry point of the script. Gets the parameters from the scripting service, makes the figure and
returns the output to the client.
def __init__(self, name, optional = False, out = False, description = None, type = None, min = None, max = None, values = None)
"""
formats = wrap(formatMap.keys()) # wrap each key in it's rtype
ckeys = COLOURS.keys()
ckeys = ckeys
ckeys.sort()
cOptions = wrap(ckeys)
dataTypes = [rstring("Image")]
client = scripts.client(
'Make_Movie',
'MakeMovie creates a movie of the image and attaches it to the originating image.',
scripts.String("Data_Type",
optional=False,
grouping="1",
description="Choose Images via their 'Image' IDs.",
values=dataTypes,
default="Image"),
scripts.List("IDs",
optional=False,
grouping="1",
description="List of Image IDs to process.").ofType(
rlong(0)),
scripts.Long("RenderingDef_ID",
description="The Rendering Definitions for the Image.",
default=-1,
optional=True,
grouping="1"),
scripts.String("Movie_Name",
description="The name of the movie",
grouping="2"),
scripts.Int(
"Z_Start",
description=
"Projection range (if not specified, use defaultZ only - no projection)",
min=0,
default=0,
grouping="3.1"),
scripts.Int(
"Z_End",
description=
"Projection range (if not specified or, use defaultZ only - no projection)",
min=0,
grouping="3.2"),
scripts.Int("T_Start",
description="The first time-point",
min=0,
default=0,
grouping="4.1"),
scripts.Int("T_End",
description="The last time-point",
min=0,
grouping="4.2"),
scripts.List("Channels",
description="The selected channels",
grouping="5").ofType(rint(0)),
scripts.Bool("Show_Time",
description="If true, display the time.",
default=True,
grouping="6"),
scripts.Bool(
"Show_Plane_Info",
description=
"If true, display the information about the plane e.g. Exposure Time.",
default=True,
grouping="7"),
scripts.Int("FPS",
description="Frames Per Second.",
default=2,
grouping="8"),
scripts.Int(
"Scalebar",
description=
"Scale bar size in microns. Only shown if image has pixel-size info.",
min=1,
grouping="9"),
scripts.String("Format",
description="Format to save movie",
values=formats,
default=QT,
grouping="10"),
scripts.String("Overlay_Colour",
description="The colour of the scalebar.",
default='White',
values=cOptions,
grouping="11"),
scripts.String(
"Canvas_Colour",
description="The background colour when using minimum size.",
default='Black',
values=cOptions),
scripts.Int("Min_Width",
description="Minimum width for output movie.",
default=-1),
scripts.Int("Min_Height",
description="Minimum height for output movie.",
default=-1),
scripts.Map(
"Plane_Map",
description=
"Specify the individual planes (instead of using T_Start, T_End, Z_Start and Z_End)",
grouping="12"),
scripts.Object(
"Watermark",
description=
"Specifiy a watermark as an Original File (png or jpeg)",
default=omero.model.OriginalFileI()),
scripts.Object(
"Intro_Slide",
description=
"Specifiy an Intro slide as an Original File (png or jpeg)",
default=omero.model.OriginalFileI()),
scripts.Int(
"Intro_Duration",
default=3,
description="Duration of Intro in seconds. Default is 3 secs."),
scripts.Object(
"Ending_Slide",
description=
"Specifiy a finishing slide as an Original File, (png or jpeg)",
default=omero.model.OriginalFileI()),
scripts.Int(
"Ending_Duration",
default=3,
description=
"Duration of finishing slide in seconds. Default is 3 secs."),
scripts.Bool(
"Do_Link",
description=
"If true, creates a FileAnnotation with the OriginalFile holding the movie and links it to the Image.",
default=True),
version="4.2.0",
authors=["Donald MacDonald", "OME Team"],
institutions=["University of Dundee"],
contact="*****@*****.**",
)
try:
conn = BlitzGateway(client_obj=client)
commandArgs = {}
for key in client.getInputKeys():
if client.getInput(key):
commandArgs[key] = client.getInput(key, unwrap=True)
print commandArgs
fileAnnotation, message = writeMovie(commandArgs, conn)
# return this fileAnnotation to the client.
client.setOutput("Message", rstring(message))
if fileAnnotation is not None:
client.setOutput("File_Annotation", robject(fileAnnotation))
finally:
client.closeSession()
