How to use the identify.Identify function in identify

To help you get started, we’ve selected a few identify examples, based on popular ways it is used in public projects.

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github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / identifyobjectsmanually.py View on Github external
import numpy as np

import cellprofiler.cpmodule as cpm
import cellprofiler.objects as cpo
import cellprofiler.preferences as cpprefs
import identify as I
import cellprofiler.settings as cps
from cellprofiler.cpmath.outline import outline
from cellprofiler.cpmath.cpmorphology import draw_line
from cellprofiler.cpmath.cpmorphology import fill_labeled_holes

TOOL_OUTLINE = "Outline"
TOOL_ZOOM_IN = "Zoom in"
TOOL_ERASE = "Erase"

class IdentifyObjectsManually(I.Identify):
    
    category = "Object Processing"
    module_name = "IdentifyObjectsManually"
    variable_revision_number = 1
    
    def create_settings(self):
        self.image_name = cps.ImageNameSubscriber(
            "Select the input image", "None",
            doc = """Choose the name of the image to display in the object
            selection user interface.""")
        
        self.objects_name = cps.ObjectNameProvider(
            "Name the objects to be identified", "Cells",
            doc = """What do you want to call the objects
            that you identify using this module? You can use this name to
            refer to your objects in subsequent modules.""")
github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / identifysecondaryobjects.py View on Github external
import cellprofiler.settings as cps
import identify as cpmi
import cellprofiler.cpmath.threshold as cpthresh
from cellprofiler.cpmath.propagate import propagate
from cellprofiler.cpmath.cpmorphology import fill_labeled_holes
from cellprofiler.cpmath.cpmorphology import fixup_scipy_ndimage_result as fix
from cellprofiler.cpmath.watershed import fast_watershed as watershed
from cellprofiler.cpmath.outline import outline

M_PROPAGATION = "Propagation"
M_WATERSHED_G = "Watershed"
M_WATERSHED_I = "Watershed - Image"
M_DISTANCE_N = "Distance - N"
M_DISTANCE_B = "Distance - B"

class IdentifySecondaryObjects(cpmi.Identify):

    module_name = "IdentifySecondaryObjects"
    variable_revision_number = 4
    category = "Object Processing"
    
    def create_settings(self):
        self.primary_objects = cps.ObjectNameSubscriber("Select the input objects","Nuclei",doc="""
            What did you call the objects you want to use as "seeds" to identify a secondary 
            object around each one? By definition, each primary object must be associated with exactly one 
            secondary object and completely contained within it.""")
        
        self.objects_name = cps.ObjectNameProvider("Name the objects to be identified","Cells")
        
        self.method = cps.Choice("Select the method to identify the secondary objects",
                                 [M_PROPAGATION, M_WATERSHED_G, M_WATERSHED_I, 
                                  M_DISTANCE_N, M_DISTANCE_B],
github dmroeder / pylogix / identify.py View on Github external
# addresses and build a list of all the devices that reply
  for ip in addresses:
	if ip[0]==2:  # IP v4
	  # create a socket
	  s=socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
	  s.settimeout(0.5)
	  s.setsockopt(socket.SOL_SOCKET, socket.SO_BROADCAST, 1)
	  s.bind((ip[4][0], 0))
	  s.sendto(request, ('255.255.255.255', 44818))
	  try:
		while(1):
		  ret=s.recv(1024)
		  context=unpack_from('
github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / editobjectsmanually.py View on Github external
import cellprofiler.objects as cpo
import cellprofiler.settings as cps
import cellprofiler.workspace as cpw
from cellprofiler.cpmath.outline import outline

import identify as I

###########################################
#
# Choices for the "do you want to renumber your objects" setting
#
###########################################
R_RENUMBER = "Renumber"
R_RETAIN = "Retain"

class EditObjectsManually(I.Identify):
    category = "Object Processing"
    variable_revision_number = 1
    module_name = 'EditObjectsManually'
    
    def create_settings(self):
        """Create your settings by subclassing this function
        
        create_settings is called at the end of initialization.
        
        You should create the setting variables for your module here:
            # Ask the user for the input image
            self.image_name = cellprofiler.settings.ImageNameSubscriber(...)
            # Ask the user for the name of the output image
            self.output_image = cellprofiler.settings.ImageNameProvider(...)
            # Ask the user for a parameter
            self.smoothing_size = cellprofiler.settings.Float(...)
github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / maskobjects.py View on Github external
"Image": MC_IMAGE,
    "Keep overlapping region": P_MASK,
    "Remove": P_REMOVE,
    "Remove depending on overlap": P_REMOVE_PERCENTAGE,
    "Keep": P_KEEP,
    "Retain": R_RETAIN,
    "Renumber": R_RENUMBER
    }
def s_lookup(x):
    '''Look up the current value for a setting choice w/backwards compatibility
    
    x - setting value from pipeline
    '''
    return S_DICTIONARY.get(x, x)

class MaskObjects(I.Identify):
    
    category = "Object Processing"
    module_name = "MaskObjects"
    variable_revision_number = 1
    
    def create_settings(self):
        '''Create the settings that control this module'''
        self.object_name = cps.ObjectNameSubscriber(
            "Select objects to be masked","None",
            doc="""Select the objects that will be masked (that is, excluded in whole 
            or in part based on the other settings in the module). 
            You can choose from any objects created by
            a previous object processing module, such as <b>IdentifyPrimaryObjects</b>,
            <b>IdentifySecondaryObjects</b> or <b>IdentifyTertiaryObjects</b>.""")
        
        self.remaining_objects = cps.ObjectNameProvider(
github CellProfiler / CellProfiler / pyCellProfiler / cellprofiler / modules / identifyprimaryobjects.py View on Github external
SMOOTHING_SIZE_VAR              = 12
MAXIMA_SUPPRESSION_SIZE_VAR     = 13
LOW_RES_MAXIMA_VAR              = 14
SAVE_OUTLINES_VAR               = 15
FILL_HOLES_OPTION_VAR           = 16
TEST_MODE_VAR                   = 17
AUTOMATIC_SMOOTHING_VAR         = 18
AUTOMATIC_MAXIMA_SUPPRESSION    = 19
MANUAL_THRESHOLD_VAR            = 20
BINARY_IMAGE_VAR                = 21

LIMIT_NONE = "Continue"
LIMIT_TRUNCATE = "Truncate"
LIMIT_ERASE = "Erase"

class IdentifyPrimaryObjects(cpmi.Identify):
            
    variable_revision_number = 6
    category =  "Object Processing"
    module_name = "IdentifyPrimaryObjects"
    
    def create_settings(self):
        self.image_name = cps.ImageNameSubscriber(
            "Select the input image",doc="""
            What did you call the images you want to use to identify objects?""")
        
        self.object_name = cps.ObjectNameProvider(
            "Name the primary objects to be identified",
            "Nuclei",doc="""
            What do you want to call the objects identified by this module?""")
        
        self.size_range = cps.IntegerRange(