Module Expr Str Import alias Assign NameStore Call AttributeLoad NameLoad attr NameLoad ImportFrom alias Import alias identifier Import alias Import alias ImportFrom alias ImportFrom alias alias Expr Str Assign NameStore Str Expr Str Assign NameStore Str Expr Str Assign NameStore Str Expr Str Assign NameStore Str FunctionDef arguments args NameParam defaults body Expr Str If UnaryOpNot Call AttributeLoad NameLoad attr NameLoad body Return NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str TryFinally body If UnaryOpNot Call AttributeLoad NameLoad attr NameLoad body Return NameLoad Return Call AttributeLoad NameLoad attr NameLoad finalbody Expr Call AttributeLoad NameLoad attr decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad Dict body Expr Str Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr CompareIsNot NameLoad NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr ListLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Dict Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr ListLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr ListLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad ClassDef bases NameLoad body Pass decorator_list Assign AttributeStore NameLoad attr Call NameLoad Expr Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr decorator_list FunctionDef arguments args NameParam defaults body Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return AttributeLoad NameLoad attr decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return AttributeLoad NameLoad attr decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return AttributeLoad NameLoad attr decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Return Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return AttributeLoad NameLoad attr decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Expr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str If CompareIsNot AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str If UnaryOpNot Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Raise Call NameLoad BinOpMod Str NameLoad Return SubscriptLoad AttributeLoad NameLoad attr Index NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults NameLoad body Expr Str If CompareIs NameLoad NameLoad body Assign NameStore Dict Assign AttributeStore NameLoad attr NameLoad Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str If AttributeLoad NameLoad attr body Return AttributeLoad NameLoad attr Return NameLoad decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return CompareIsNot AttributeLoad NameLoad attr NameLoad decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam defaults body Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad decorator_list Assign NameStore Call NameLoad NameLoad NameLoad FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Import alias identifier Import alias identifier Assert UnaryOpNot AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad If Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad NameLoad orelse Assign NameStore BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad If AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr BoolOpOr NameLoad AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad orelse Assign NameStore Call AttributeLoad NameLoad attr BoolOpOr NameLoad AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad If UnaryOpNot CompareIn NameLoad AttributeLoad NameLoad attr body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad NameLoad NameLoad body Expr Str Import alias identifier Assert UnaryOpNot AttributeLoad NameLoad attr If CompareIs NameLoad NameLoad body Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr If CompareIs NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr If AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword NameLoad keyword NameLoad orelse Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword NameLoad If UnaryOpNot CompareIn NameLoad AttributeLoad NameLoad attr body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return Call AttributeLoad AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Return SubscriptLoad AttributeLoad NameLoad attr Index NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return AttributeLoad NameLoad attr decorator_list Assign NameStore Call NameLoad NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults vararg kwarg body Expr Str Import alias identifier If CompareIn Str NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Delete SubscriptDel NameLoad Index Str Assign NameStore SubscriptLoad NameLoad Index Str Assign NameStore NameLoad orelse Assign NameStore NameLoad If CompareIs AttributeLoad NameLoad attr NameLoad body If BoolOpAnd Call AttributeLoad NameLoad attr UnaryOpNot NameLoad body Raise Call AttributeLoad NameLoad attr orelse Return Call AttributeLoad NameLoad attr NameLoad NameLoad orelse Return Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str If CompareIs AttributeLoad NameLoad attr NameLoad body Raise Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str If CompareIsNot AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr orelse If CompareIsNot AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str If CompareIsNot AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad orelse If CompareIsNot AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad BinOpAdd AttributeLoad AttributeLoad NameLoad attr attr Num AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return CompareEq AttributeLoad AttributeLoad NameLoad attr attr BinOpSub Call AttributeLoad AttributeLoad NameLoad attr attr Num decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad For NameStore AttributeLoad NameLoad attr body Expr Call NameLoad NameLoad decorator_list Assign NameStore Call NameLoad NameLoad NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list ClassDef bases NameLoad body Pass decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Import alias ImportFrom alias alias alias Import alias identifier ImportFrom alias alias Assign NameStore NameLoad If CompareIsNot AttributeLoad NameLoad attr NameLoad body Assign NameStore CompareEq Call NameLoad AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad TryFinally body Assign TupleStore NameStore AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr keyword Str If CompareIsNot AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call NameLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr If BoolOpAnd NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad attr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call NameLoad NameLoad orelse If NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr orelse Assign NameStore Call NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad keyword NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call AttributeLoad NameLoad attr For TupleStore NameStore NameStore TupleLoad TupleLoad NameLoad NameLoad TupleLoad NameLoad NameLoad body If Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr NameLoad body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad AttributeLoad NameLoad attr NameLoad If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Expr Call NameLoad NameLoad If NameLoad body Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr finalbody Assign AttributeStore NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str ImportFrom alias alias If Call NameLoad AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr Assign TupleStore NameStore AttributeStore NameLoad attr Call NameLoad Assign AttributeStore NameLoad attr Call NameLoad keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr NameLoad If CompareIsNot AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call NameLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword Str For NameStore NameLoad body Assign NameStore SubscriptLoad NameLoad Index NameLoad If Call NameLoad NameLoad AttributeLoad NameLoad attr body Assign SubscriptStore NameLoad Index NameLoad AttributeLoad NameLoad attr orelse Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad NameLoad NameLoad For NameStore AttributeLoad NameLoad attr body Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str If BoolOpAnd CompareIsNot AttributeLoad NameLoad attr NameLoad CompareIsNot AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body ImportFrom alias Assign NameStore Call NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad keyword NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam defaults body ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call NameLoad decorator_list FunctionDef arguments args NameParam defaults body If UnaryOpNot AttributeLoad NameLoad attr body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults NameLoad body Expr Str Import alias identifier If BoolOpOr CompareEq Call NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Num NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore NameLoad If BoolOpAnd CompareGt Call NameLoad NameLoad Num UnaryOpNot Call AttributeLoad SubscriptLoad NameLoad Index Num attr body For TupleStore NameStore NameStore Call NameLoad SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Slice Num SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Slice Num body If Call AttributeLoad NameLoad attr body Assign NameStore NameLoad Assign NameStore CompareIs AttributeLoad NameLoad attr NameLoad If NameLoad body ImportFrom alias Assign AttributeStore NameLoad attr Call NameLoad TryFinally body TryExcept body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad Return NameLoad handlers ExceptHandler body Expr Call AttributeLoad NameLoad attr Str keyword Num Return NameLoad finalbody If NameLoad body Assign AttributeStore NameLoad attr NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body For NameStore AttributeLoad NameLoad attr body TryExcept body Expr Call NameLoad NameLoad handlers ExceptHandler body Expr Call AttributeLoad NameLoad attr Str keyword Num decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad Call NameLoad AttributeLoad NameLoad attr NameLoad attr NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad Call NameLoad AttributeLoad NameLoad attr NameLoad attr NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad Call NameLoad AttributeLoad NameLoad attr NameLoad attr NameLoad decorator_list decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad decorator_list decorator_list
N/A N/A workspace.py - the workspace for an imageset
 N/A logging N/A logger N/A N/A logging getLogger __name__ cStringIO StringIO N/A numpy np N/A h5py N/A os cellprofiler.cpgridinfo CPGridInfo utilities.hdf5_dict HDF5FileList HDF5Dict N/A Continue to run the pipeline

Set workspace.disposition to DISPOSITION_CONTINUE to go to the next module.
This is the default.
 N/A DISPOSITION_CONTINUE Continue N/A Skip remaining modules

Set workspace.disposition to DISPOSITION_SKIP to skip to the next image set
in the pipeline.
 N/A DISPOSITION_SKIP Skip N/A Pause and let the UI run

Set workspace.disposition to DISPOSITION_PAUSE to pause the UI. Set
it back to DISPOSITION_CONTINUE to resume.
 N/A DISPOSITION_PAUSE Pause N/A Cancel running the pipeline N/A DISPOSITION_CANCEL Cancel is_workspace_file N/A N/A path N/A N/A N/A Return True if the file along the given path is a workspace file N/A N/A N/A N/A h5py is_hdf5 path N/A N/A False N/A h5file N/A N/A h5py File path mode r N/A N/A N/A N/A N/A N/A HDF5FileList has_file_list h5file N/A N/A False N/A N/A N/A HDF5Dict has_hdf5_dict h5file N/A N/A N/A N/A h5file close N/A Workspace N/A object N/A N/A The workspace contains the processing information and state for
    a pipeline run on an image set
     __init__ N/A N/A self pipeline module image_set object_set measurements image_set_list frame create_new_window outlines N/A None False N/A N/A N/A Workspace constructor

        pipeline          - the pipeline of modules being run
        module            - the current module to run (a CPModule instance)
        image_set         - the set of images available for this iteration
                            (a cpimage.ImageSet instance)
        object_set        - an object.ObjectSet instance
        image_set_list    - the list of all images
        frame             - the application's frame, or None for no display
        create_new_window - True to create another frame, even if one is open
                            False to reuse the current frame.
         N/A N/A self __pipeline pipeline N/A N/A self __module module N/A N/A self __image_set image_set N/A N/A self __object_set object_set N/A N/A self __measurements measurements N/A N/A self __image_set_list image_set_list N/A N/A self __frame frame N/A N/A self __do_show N/A frame None N/A N/A self __outlines outlines N/A N/A self __windows_used N/A N/A N/A self __create_new_window create_new_window N/A N/A self __grid N/A N/A N/A self __disposition DISPOSITION_CONTINUE N/A N/A self __disposition_listeners N/A N/A N/A self __in_background False N/A N/A self __filename None N/A N/A self __file_list None N/A N/A self __loading False N/A N/A measurements None N/A N/A N/A N/A self set_file_list N/A HDF5FileList N/A N/A measurements hdf5_dict hdf5_file N/A N/A self __notification_callbacks N/A N/A N/A self interaction_handler None N/A N/A self post_run_display_handler None N/A N/A self post_group_display_handler None N/A N/A self cancel_handler None DisplayData N/A object N/A N/A N/A N/A N/A self display_data N/A DisplayData N/A Object into which the module's run() method can stuff items
        that must be available later for display(). N/A refresh N/A N/A self N/A N/A N/A Refresh any windows created during use N/A window N/A self __windows_used N/A N/A N/A N/A N/A N/A window figure canvas draw N/A get_windows_used N/A N/A self N/A N/A N/A N/A self __windows_used N/A get_pipeline N/A N/A self N/A N/A N/A Get the pipeline being run N/A N/A self __pipeline N/A N/A pipeline N/A property get_pipeline get_image_set N/A N/A self N/A N/A N/A The image set is the set of images currently being processed
         N/A N/A self __image_set N/A set_image_set_for_testing_only N/A N/A self image_set_number N/A N/A N/A N/A self __image_set N/A N/A N/A self image_set_list get_image_set image_set_number N/A N/A image_set N/A property get_image_set get_image_set_list N/A N/A self N/A N/A N/A The list of all image sets N/A N/A self __image_set_list N/A N/A image_set_list N/A property get_image_set_list get_object_set N/A N/A self N/A N/A N/A The object set is the set of image labels for the current image set
         N/A N/A self __object_set N/A N/A object_set N/A property get_object_set get_objects N/A N/A self objects_name N/A N/A N/A Return the objects.Objects instance for the given name.

        objects_name - the name of the objects to retrieve
         N/A N/A N/A N/A self object_set get_objects objects_name N/A get_measurements N/A N/A self N/A N/A N/A The measurements contain measurements made on images and objects
         N/A N/A self __measurements N/A N/A measurements N/A property get_measurements add_measurement N/A N/A self object_name feature_name data N/A N/A N/A Add a measurement to the workspace's measurements

        object_name - name of the objects measured or 'Image'
        feature_name - name of the feature measured
        data - the result of the measurement
         N/A N/A N/A N/A self measurements add_measurement object_name feature_name data N/A get_file_list N/A N/A self N/A N/A N/A The user-curated list of files N/A N/A self __file_list N/A set_file_list N/A N/A self file_list N/A N/A N/A Set the file list

        A caller can set the file list to the file list in some other
        workspace. This lets a single, sometimes very bulky file list be
        used without copying it to a measurements file.
         N/A N/A N/A self __file_list None N/A N/A N/A N/A N/A self __file_list remove_notification_callback N/A self __on_file_list_changed N/A N/A self __file_list file_list N/A N/A file_list None N/A N/A N/A N/A N/A self __file_list add_notification_callback N/A self __on_file_list_changed N/A N/A file_list N/A property get_file_list get_grid N/A N/A self grid_name N/A N/A N/A Return a grid with the given name N/A N/A N/A N/A N/A self __grid has_key grid_name N/A N/A N/A ValueError N/A Could not find grid %s grid_name N/A N/A N/A self __grid N/A grid_name N/A set_grids N/A N/A self last N/A None N/A N/A Initialize the grids for an image set

        last - none if first in image set or the return value from
               this method.
        returns a grid dictionary
         N/A N/A last None N/A N/A last N/A N/A N/A self __grid last N/A N/A self __grid N/A set_grid N/A N/A self grid_name grid_info N/A N/A N/A Add a grid to the workspace N/A N/A N/A self __grid N/A grid_name grid_info N/A cache N/A N/A self N/A N/A N/A N/A N/A N/A self measurements cache N/A N/A N/A N/A self measurements cache_object_set N/A self object_set N/A get_frame N/A N/A self N/A N/A N/A The frame is CellProfiler's gui window

        If the frame is present, a module should do its display
         N/A N/A self __do_show N/A N/A N/A self __frame N/A None N/A N/A frame N/A property get_frame show_frame N/A N/A self do_show N/A N/A N/A N/A self __do_show do_show N/A get_display N/A N/A self N/A N/A N/A True to provide a gui display N/A N/A N/A self __frame None N/A N/A display N/A property get_display get_in_background N/A N/A self N/A N/A N/A N/A self __in_background N/A set_in_background N/A N/A self val N/A N/A N/A N/A self __in_background val N/A N/A in_background N/A property get_in_background set_in_background get_module_figure N/A N/A self module image_set_number parent N/A None N/A N/A Create a CPFigure window or find one already created N/A cellprofiler.gui.cpfigure cpf N/A cellprofiler.measurements cpmeas N/A N/A N/A self __in_background N/A window_name N/A N/A cpf window_name module N/A N/A N/A N/A self measurements has_feature N/A cpmeas EXPERIMENT N/A cpmeas M_GROUPING_TAGS N/A N/A group_number N/A N/A self measurements N/A N/A N/A cpmeas IMAGE N/A cpmeas GROUP_NUMBER image_set_number N/A group_index N/A N/A self measurements N/A N/A N/A cpmeas IMAGE N/A cpmeas GROUP_INDEX image_set_number N/A title N/A %s #%d, image cycle #%d, group #%d, group index #%d N/A N/A module module_name N/A module module_num image_set_number group_number group_index N/A N/A title N/A %s #%d, image cycle #%d N/A N/A module module_name N/A module module_num image_set_number N/A N/A self __create_new_window N/A N/A figure N/A N/A cpf CPFigureFrame N/A parent N/A self __frame name window_name title title N/A N/A figure N/A N/A cpf create_or_find N/A parent N/A self __frame name window_name title title N/A N/A N/A figure N/A self __windows_used N/A N/A N/A N/A N/A self __windows_used append figure N/A figure N/A create_or_find_figure N/A N/A self title subplots window_name N/A None None None N/A N/A Create a matplotlib figure window or find one already created N/A cellprofiler.gui.cpfigure cpf N/A N/A N/A self __in_background N/A N/A title None N/A N/A title N/A N/A self __module module_name N/A N/A window_name None N/A N/A window_name N/A N/A cpf window_name N/A self __module N/A N/A self __create_new_window N/A N/A figure N/A N/A cpf CPFigureFrame self title title name window_name subplots subplots N/A N/A figure N/A N/A cpf create_or_find N/A self __frame title title name window_name subplots subplots N/A N/A N/A figure N/A self __windows_used N/A N/A N/A N/A N/A self __windows_used append figure N/A figure N/A get_outline_names N/A N/A self N/A N/A N/A The names of outlines of objects N/A N/A N/A N/A self __outlines keys N/A add_outline N/A N/A self name outline N/A N/A N/A Add an object outline to the workspace N/A N/A N/A self __outlines N/A name outline N/A get_outline N/A N/A self name N/A N/A N/A Get a named outline N/A N/A N/A self __outlines N/A name N/A get_module N/A N/A self N/A N/A N/A Get the module currently being run N/A N/A self __module N/A N/A module N/A property get_module set_module N/A N/A self module N/A N/A N/A Set the module currently being run N/A N/A self __module module N/A interaction_request N/A N/A self module N/A args kwargs N/A N/A make a request for GUI interaction via a pipeline event

        module - target module for interaction request

        headless_ok - True if the interaction request can be made in
                      a headless context. An example is synchronized access to
                      a shared resource which must be coordinated among all
                      workers.
         N/A cellprofiler.preferences cpprefs N/A N/A headless_ok kwargs N/A N/A tmp N/A N/A kwargs copy N/A N/A tmp N/A headless_ok N/A headless_ok N/A kwargs N/A headless_ok N/A kwargs tmp N/A N/A headless_ok False N/A N/A N/A self interaction_handler None N/A N/A N/A N/A N/A cpprefs get_headless N/A headless_ok N/A N/A N/A N/A self NoInteractionException N/A N/A N/A N/A module handle_interaction args kwargs N/A N/A N/A N/A self interaction_handler module args kwargs N/A cancel_request N/A N/A self N/A N/A N/A Make a request to cancel an ongoing analysis N/A N/A N/A self cancel_handler None N/A N/A N/A N/A self NoInteractionException N/A N/A N/A self cancel_handler N/A post_group_display N/A N/A self module N/A N/A N/A Perform whatever post-group module display is necessary

        module - module being run
         N/A N/A N/A self post_group_display_handler None N/A N/A N/A N/A self post_group_display_handler module N/A self display_data N/A N/A self measurements image_set_number N/A N/A N/A N/A self frame None N/A N/A figure N/A N/A self get_module_figure module N/A N/A self measurements image_set_number N/A self frame N/A N/A N/A module display_post_group self figure N/A post_run_display N/A N/A self module N/A N/A N/A Perform whatever post-run module display is necessary

        module - module being run
         N/A N/A N/A self post_run_display_handler None N/A N/A N/A N/A self post_run_display_handler self module N/A N/A N/A N/A self frame None N/A N/A figure N/A N/A self get_module_figure module N/A N/A N/A self measurements image_set_count 1 N/A self frame N/A N/A N/A module display_post_run self figure N/A is_last_image_set N/A N/A self N/A N/A N/A N/A N/A N/A self measurements image_set_number N/A N/A N/A N/A self image_set_list count 1 N/A property get_disposition N/A N/A self N/A N/A N/A How to proceed with the pipeline

        One of the following values:
        DISPOSITION_CONTINUE - continue to execute the pipeline
        DISPOSITION_PAUSE - wait until the status changes before executing
                            the next module
        DISPOSITION_CANCEL - stop running the pipeline
        DISPOSITION_SKIP - skip the rest of this image set
         N/A N/A self __disposition N/A set_disposition N/A N/A self disposition N/A N/A N/A N/A self __disposition disposition N/A event N/A DispositionChangedEvent disposition N/A listener N/A self __disposition_listeners N/A N/A N/A listener event N/A N/A disposition N/A property get_disposition set_disposition add_disposition_listener N/A N/A self listener N/A N/A N/A N/A N/A N/A self __disposition_listeners append listener N/A NoInteractionException N/A Exception N/A N/A N/A load N/A N/A self filename load_pipeline N/A N/A N/A Load a workspace from a .cpi file

        filename - path to file to load

        load_pipeline - true to load the pipeline from the file, false to
                        use the current pipeline.
         N/A shutil pipeline M_PIPELINE M_DEFAULT_INPUT_FOLDER M_DEFAULT_OUTPUT_FOLDER N/A cellprofiler.measurements cpmeas cellprofiler.preferences set_default_image_directory set_default_output_directory N/A image_set_and_measurements_are_same False N/A N/A N/A self __measurements None N/A N/A image_set_and_measurements_are_same N/A N/A id N/A self __measurements N/A id N/A self __image_set N/A N/A N/A self close N/A N/A self __loading True N/A N/A N/A N/A fd N/A self __filename N/A N/A cpmeas make_temporary_file N/A N/A N/A os close fd N/A N/A N/A shutil copyfile filename N/A self __filename N/A N/A self __measurements N/A N/A cpmeas Measurements filename N/A self __filename mode r+ N/A N/A N/A self __file_list None N/A N/A N/A N/A N/A self __file_list remove_notification_callback N/A self __on_file_list_changed N/A N/A self __file_list N/A HDF5FileList N/A N/A N/A self measurements hdf5_dict hdf5_file N/A N/A N/A N/A self __file_list add_notification_callback N/A self __on_file_list_changed N/A N/A load_pipeline N/A N/A N/A self __measurements has_feature N/A cpmeas EXPERIMENT M_PIPELINE N/A N/A pipeline_txt N/A N/A N/A N/A N/A self __measurements get_experiment_measurement M_PIPELINE encode utf-8 N/A N/A N/A N/A self pipeline load N/A StringIO pipeline_txt N/A N/A load_pipeline N/A N/A N/A N/A N/A self pipeline clear N/A N/A fd N/A StringIO N/A N/A N/A N/A self pipeline savetxt fd save_image_plane_details False N/A N/A N/A N/A self __measurements add_experiment_measurement M_PIPELINE N/A N/A fd getvalue N/A N/A feature function N/A N/A M_DEFAULT_INPUT_FOLDER set_default_image_directory N/A M_DEFAULT_OUTPUT_FOLDER set_default_output_directory N/A N/A N/A N/A N/A self measurements has_feature N/A cpmeas EXPERIMENT feature N/A N/A path N/A N/A self measurements N/A N/A N/A cpmeas EXPERIMENT feature N/A N/A N/A N/A os path isdir path N/A N/A N/A function path N/A image_set_and_measurements_are_same N/A N/A N/A self __image_set N/A self __measurements N/A N/A N/A self __loading False N/A N/A N/A self notify N/A N/A self WorkspaceLoadedEvent self N/A create N/A N/A self N/A N/A N/A Create a new workspace file

        filename - name of the workspace file
         measurements Measurements make_temporary_file N/A N/A isinstance N/A self measurements Measurements N/A N/A N/A N/A self close N/A N/A fd N/A self __filename N/A make_temporary_file N/A N/A self __measurements N/A Measurements filename N/A self __filename mode w N/A N/A N/A os close fd N/A N/A N/A self __file_list None N/A N/A N/A N/A N/A self __file_list remove_notification_callback N/A self __on_file_list_changed N/A N/A self __file_list N/A HDF5FileList N/A N/A N/A self measurements hdf5_dict hdf5_file N/A N/A N/A N/A self __file_list add_notification_callback N/A self __on_file_list_changed N/A N/A N/A self notify N/A N/A self WorkspaceCreatedEvent self N/A save N/A N/A self path N/A N/A N/A Save the current workspace to the given path

        path - path to file to save

        Note: "saving" means copying the temporary workspace file
         N/A N/A N/A self save_default_folders_to_measurements N/A N/A N/A N/A self measurements flush N/A hdf5src N/A N/A N/A self measurements hdf5_dict hdf5_file N/A hdf5dest N/A N/A h5py File path mode w N/A key hdf5src N/A N/A obj N/A hdf5src N/A key N/A N/A isinstance obj N/A h5py Dataset N/A N/A N/A hdf5dest N/A key N/A obj value N/A N/A N/A N/A hdf5src copy N/A hdf5src N/A key hdf5dest key N/A key N/A hdf5src attrs N/A N/A N/A N/A hdf5dest attrs N/A key N/A N/A hdf5src attrs N/A key N/A N/A N/A hdf5dest close N/A close N/A N/A self N/A N/A N/A Close the workspace and delete the temporary measurements file N/A N/A N/A N/A self measurements None N/A N/A self __filename None N/A N/A N/A N/A N/A self measurements close N/A N/A N/A os unlink N/A self __filename N/A save_pipeline_to_measurements N/A N/A self N/A N/A cellprofiler.pipeline M_PIPELINE N/A fd N/A StringIO N/A N/A N/A N/A self pipeline savetxt fd save_image_plane_details False N/A N/A N/A N/A self measurements add_experiment_measurement M_PIPELINE N/A N/A fd getvalue N/A N/A N/A N/A self measurements flush N/A save_default_folders_to_measurements N/A N/A self N/A N/A cellprofiler.pipeline M_DEFAULT_INPUT_FOLDER cellprofiler.pipeline M_DEFAULT_OUTPUT_FOLDER cellprofiler.preferences get_default_image_directory cellprofiler.preferences get_default_output_directory N/A N/A N/A N/A self measurements add_experiment_measurement M_DEFAULT_INPUT_FOLDER N/A get_default_image_directory N/A N/A N/A N/A self measurements add_experiment_measurement M_DEFAULT_OUTPUT_FOLDER N/A get_default_output_directory N/A invalidate_image_set N/A N/A self N/A N/A N/A N/A N/A self __loading N/A N/A N/A N/A N/A self measurements clear N/A N/A N/A self save_pipeline_to_measurements N/A refresh_image_set N/A N/A self force N/A False N/A N/A Refresh the image set if not present

        force - force a rewrite, even if the image set is cached

        This method executes Pipeline.prepare_run in order on self in order
        to write the image set image measurements to our internal
        measurements. If image set measurements are present, then we
        assume that the cache reflects pipeline + file list unless "force"
        is true.
         N/A cellprofiler.measurements cpmeas N/A N/A N/A N/A len N/A N/A N/A self measurements get_image_numbers 0 force N/A N/A N/A N/A N/A self measurements clear N/A N/A N/A self save_pipeline_to_measurements N/A modules N/A N/A N/A self pipeline modules N/A stop_module None N/A N/A N/A N/A len modules 1 N/A N/A N/A N/A modules N/A -1 is_load_module N/A N/A N/A module next_module N/A zip N/A N/A N/A N/A self pipeline modules N/A -1 N/A N/A N/A N/A self pipeline modules N/A 1 N/A N/A N/A N/A module is_load_module N/A N/A stop_module next_module N/A no_image_set_list N/A N/A self image_set_list None N/A no_image_set_list N/A cellprofiler.cpimage ImageSetList N/A N/A self __image_set_list N/A ImageSetList N/A N/A N/A N/A N/A result N/A N/A N/A self pipeline prepare_run self stop_module N/A result N/A N/A N/A N/A N/A N/A logger error Failed during prepare_run exc_info 1 N/A False N/A N/A no_image_set_list N/A N/A N/A self __image_set_list None N/A True N/A add_notification_callback N/A N/A self callback N/A N/A N/A Add a callback that will be called on a workspace event

        Workspace events are load events, and file list events.

        callback - a function to be called when an event occurs. The signature
        is: callback(event)
         N/A N/A N/A N/A self __notification_callbacks append callback N/A remove_notification_callback N/A N/A self callback N/A N/A N/A N/A N/A N/A self __notification_callbacks remove callback N/A notify N/A N/A self event N/A N/A N/A callback N/A self __notification_callbacks N/A N/A N/A N/A N/A callback event N/A N/A N/A N/A N/A N/A logger error Notification callback threw an exception exc_info 1 N/A __on_file_list_changed N/A N/A self N/A N/A N/A N/A N/A self notify N/A N/A self WorkspaceFileListNotification self N/A WorkspaceEvent N/A object N/A N/A The base for any event sent to a workspace callback via Workspace.notify

         __init__ N/A N/A self workspace N/A N/A N/A N/A self workspace workspace N/A N/A WorkspaceLoadedEvent N/A WorkspaceEvent N/A N/A Indicates that a workspace has been loaded

        When a workspace loads, the file list changes.
         __init__ N/A N/A self workspace N/A N/A N/A N/A N/A N/A super N/A self __class__ self __init__ workspace N/A N/A WorkspaceCreatedEvent N/A WorkspaceEvent N/A N/A Indicates that a blank workspace has been created __init__ N/A N/A self workspace N/A N/A N/A N/A N/A N/A super N/A self __class__ self __init__ workspace N/A N/A WorkspaceFileListNotification N/A WorkspaceEvent N/A N/A Indicates that the workspace's file list changed __init__ N/A N/A self workspace N/A N/A N/A N/A N/A N/A super N/A self __class__ self __init__ workspace N/A N/A N/A DispositionChangedEvent N/A object N/A __init__ N/A N/A self disposition N/A N/A N/A N/A self disposition disposition N/A N/A