Module ImportFrom alias Assign NameStore BinOpMod Str Call NameLoad Import alias identifier Import alias identifier Import alias identifier Import alias identifier Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore ListLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Assign NameStore Str ClassDef bases AttributeLoad NameLoad attr body Assign NameStore Str Assign NameStore Str Assign NameStore Num FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr keyword Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str NameLoad keyword BinOpMod Str Call NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Dict AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Num keyword Num keyword BinOpMod Str Call NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return ListLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareEq AttributeLoad NameLoad attr NameLoad body AugAssignAdd NameStore ListLoad AttributeLoad NameLoad attr Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Expr Str If CompareGt Call NameLoad NameLoad Num body Assign NameStore Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore AttributeLoad NameLoad attr If UnaryOpNot AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr NameLoad orelse Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr If AttributeLoad NameLoad attr body Assign AttributeStore AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore AttributeLoad NameLoad attr attr AttributeLoad Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign NameStore AttributeLoad NameLoad attr If CompareNotIn AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr TupleLoad Num Num If CompareEq AttributeLoad NameLoad attr Num body Expr Call AttributeLoad NameLoad attr Num Num NameLoad AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr Num Num NameLoad AttributeLoad AttributeLoad NameLoad attr attr keyword Call AttributeLoad NameLoad attr Num Num orelse Expr Call AttributeLoad NameLoad attr Num Num NameLoad AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr Num Num NameLoad AttributeLoad AttributeLoad NameLoad attr attr keyword Call AttributeLoad NameLoad attr Num Num decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body If BoolOpAnd NameLoad CompareEq NameLoad Str body Assign NameStore BinOpAdd SubscriptLoad NameLoad Slice Num NameLoad Assign NameStore NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Num If BoolOpAnd NameLoad CompareEq NameLoad Str CompareEq NameLoad Num body Assign NameStore SubscriptLoad NameLoad Slice Num Assign NameStore NameLoad Assign NameStore Num If BoolOpAnd UnaryOpNot NameLoad CompareEq NameLoad Num body Assign NameStore BinOpAdd NameLoad ListLoad Str Return TupleLoad NameLoad NameLoad NameLoad decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam defaults Num body Expr Str Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr 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 NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign NameStore SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign NameStore SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad NameLoad NameLoad Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr SubscriptLoad NameLoad Index AttributeLoad NameLoad attr Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults 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 Num Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return CompareIsNot AttributeLoad NameLoad attr NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Return AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad If AttributeLoad NameLoad attr body Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad orelse Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad AttributeLoad NameLoad attr attr Slice Num NameLoad If CompareEq AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr Assign SubscriptStore AttributeLoad NameLoad attr Index UnaryOpInvert AttributeLoad NameLoad attr Num Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore NameLoad attr BinOpPow Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Num Return If CompareEq AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr Assign SubscriptStore AttributeLoad NameLoad attr Index UnaryOpInvert AttributeLoad NameLoad attr Num Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr Call AttributeLoad Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr Num Return If CompareEq AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Return If CompareEq AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Return Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr If AttributeLoad NameLoad attr body Assign NameStore IfExp CompareEq AttributeLoad NameLoad attr NameLoad Num Num Assign SubscriptStore AttributeLoad NameLoad attr Index UnaryOpInvert AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad If AttributeLoad NameLoad attr body AugAssignAdd AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad orelse AugAssignAdd AttributeStore NameLoad attr Num If CompareIn AttributeLoad NameLoad attr ListLoad NameLoad NameLoad body If AttributeLoad NameLoad attr body AugAssignAdd SubscriptStore AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr orelse AugAssignAdd AttributeStore NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr NameLoad body If AttributeLoad NameLoad attr body Assign SubscriptStore AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr orelse Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr NameLoad body If AttributeLoad NameLoad attr body Assign SubscriptStore AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad NameLoad attr orelse Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore AttributeLoad NameLoad attr AugAssignAdd SubscriptStore AttributeLoad NameLoad attr Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad AugAssignAdd SubscriptStore AttributeLoad NameLoad attr Index NameLoad BinOpPow Call AttributeLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad attr AttributeLoad NameLoad attr Num orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad NameLoad attr BinOpDiv BinOpMult BinOpMult Num AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AugAssignAdd AttributeStore NameLoad attr Num Assign NameStore AttributeLoad NameLoad attr AugAssignAdd SubscriptStore AttributeLoad NameLoad attr Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad AugAssignAdd SubscriptStore AttributeLoad NameLoad attr Index NameLoad BinOpMult NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad AugAssignAdd SubscriptStore AttributeLoad NameLoad attr Index NameLoad NameLoad orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore BinOpDiv BinOpMult AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad Assign NameStore BinOpBitAnd CompareLt AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore BinOpBitAnd CompareGt AttributeLoad NameLoad attr NameLoad NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad SubscriptLoad NameLoad Index NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad SubscriptLoad NameLoad Index NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr BinOpBitAnd AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse Raise Call NameLoad BinOpMod Str AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore AttributeLoad NameLoad attr Assign NameStore CompareGt NameLoad Num If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore AttributeLoad NameLoad attr orelse Assign NameStore AttributeLoad NameLoad attr If CompareEq AttributeLoad NameLoad attr Num body Assign NameStore Call AttributeLoad NameLoad attr BinOpMult ListLoad NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore CompareGt NameLoad Num If CompareIsNot AttributeLoad NameLoad attr NameLoad body Return AttributeLoad NameLoad attr If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore BinOpDiv AttributeLoad NameLoad attr NameLoad orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index NameLoad BinOpDiv SubscriptLoad AttributeLoad NameLoad attr Index NameLoad SubscriptLoad NameLoad Index NameLoad AugAssignSub SubscriptStore NameLoad Index NameLoad BinOpDiv BinOpPow SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Num BinOpPow SubscriptLoad NameLoad Index NameLoad Num orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad AugAssignSub SubscriptStore NameLoad Index NameLoad BinOpDiv BinOpMult SubscriptLoad AttributeLoad NameLoad attr Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad SubscriptLoad NameLoad Index NameLoad Assign NameStore Call AttributeLoad AttributeLoad BinOpMult NameLoad Call AttributeLoad NameLoad attr NameLoad attr attr AttributeLoad NameLoad attr orelse If CompareEq AttributeLoad NameLoad attr NameLoad body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index NameLoad BinOpSub SubscriptLoad AttributeLoad NameLoad attr Index NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad orelse If BoolOpAnd CompareEq AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr UnaryOpInvert NameLoad body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Assign SubscriptStore NameLoad Index UnaryOpInvert NameLoad Num orelse Assign NameStore AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index UnaryOpInvert NameLoad Num If BoolOpOr Call AttributeLoad NameLoad attr NameLoad CompareEq AttributeLoad NameLoad attr NameLoad body Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad orelse Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Pass decorator_list decorator_list
N/A cellprofiler.gui.help LOADING_IMAGE_SEQ_HELP_REF N/A __doc__ N/A 
<b>Make Projection</b> combines several two-dimensional images of
the same field of view together, either by performing a mathematical operation
upon the pixel values at each pixel position.
<hr>
This module combines a set of images by performing a mathematic operation of your
choice at each pixel position; please refer to the settings help for more information on the available
operations. The process of averaging or summing a Z-stack (3D image stack) is known as making a projection.

<p>This module will create a projection of all images specified in the Input modules. For more
information on loading image stacks and movies, see <i>%(LOADING_IMAGE_SEQ_HELP_REF)s</i>.
To achieve per-folder projections
i.e., creating a projection for each set of images in a folder, for all input folders,
make the following setting specifications:
<ol>
<li>In the <b>Images</b> module, drag-and-drop the parent folder containing the sub-folders.</li>
<li>In the <b>Metadata</b> module, enable metadata extraction and extract metadata from the folder name
by using a regular expression to capture the subfolder name, e.g., <code>.*[\\/](?P&lt;Subfolder&gt;.*)$</code></li>
<li>In the <b>NamesAndTypes</b> module, specify the appropriate names for any desired channels.</li>
<li>In the <b>Groups</b> module, enable image grouping, and select the metadata tag representing
the sub-folder name as the metadata category.</li>
</ol>
Keep in mind that the projection image is not immediately available in subsequent modules because the
output of this module is not complete until all image processing cycles have completed. Therefore,
the projection should be created with a dedicated pipeline.</p>

See also the help for the <b>Input</b> modules.
 N/A globals N/A numpy np N/A cellprofiler.cpmodule cpm N/A cellprofiler.cpimage cpi N/A cellprofiler.settings cps N/A P_AVERAGE Average N/A P_MAXIMUM Maximum N/A P_MINIMUM Minimum N/A P_SUM Sum N/A P_VARIANCE Variance N/A P_POWER Power N/A P_BRIGHTFIELD Brightfield N/A P_MASK Mask N/A P_ALL N/A P_AVERAGE P_MAXIMUM P_MINIMUM P_SUM P_VARIANCE P_POWER P_BRIGHTFIELD P_MASK N/A K_PROVIDER Provider MakeProjection N/A N/A cpm CPModule N/A N/A module_name MakeProjection N/A category Image Processing N/A variable_revision_number 2 create_settings N/A N/A self N/A N/A N/A N/A self image_name N/A N/A cps ImageNameSubscriber Select the input image N/A cps NONE doc 
            Select the image to be made into a projection. N/A N/A self projection_type N/A N/A cps Choice Type of projection P_ALL doc N/A 
            The final projection image can be created by the following methods:
            <ul>
            <li><i>%(P_AVERAGE)s:</i> Use the average pixel intensity at each pixel position.</li>
            <li><i>%(P_MAXIMUM)s:</i> Use the maximum pixel value at each pixel position.</li>
            <li><i>%(P_MINIMUM)s:</i> Use the minimum pixel value at each pixel position.</li>
            <li><i>%(P_SUM)s:</i> Add the pixel values at each pixel position.</li>
            <li><i>%(P_VARIANCE)s:</i> Compute the variance at each pixel position. <br>
            The variance  method is described in Selinummi et al (2009).
            The method is designed to operate on a z-stack of brightfield images taken
            at different focus planes. Background pixels will have relatively uniform
            illumination whereas cytoplasm pixels will have higher variance across the
            z-stack.</li>
            <li><i>%(P_POWER)s:</i> Compute the power at a given frequency at each pixel position.<br>
            The power method is experimental. The method computes the power at a given
            frequency through the z-stack. It might be used with a phase contrast image
            where the signal at a given pixel will vary sinusoidally with depth. The
            frequency is measured in z-stack steps and pixels that vary with the given
            frequency will have a higher score than other pixels with similar variance,
            but different frequencies.</li>
            <li><i>%(P_BRIGHTFIELD)s:</i> Perform the brightfield projection at each pixel position.<br>
            Artifacts such as dust appear as black spots which are most strongly resolved
            at their focal plane with gradually increasing signals below. The brightfield
            method scores these as zero since the dark appears in the early z-stacks.
            These pixels have a high score for the variance method but have a reduced
            score when using the brightfield method.</li>
            <li><i>%(P_MASK)s:</i> Compute a binary image of the pixels that are
            masked in any of the input images.<br>
            The mask method operates on any masks that might have been applied to the
            images in a group. The output is a binary image where the "1" pixels are
            those that are not masked in all of the images and the "0" pixels are those
            that are masked in one or more of the images.<br>
            You can use the output of the mask method to mask or crop all of the
            images in a group similarly. Use the mask method to combine all of the
            masks in a group, save the image and then use <b>Crop</b>, <b>MaskImage</b> or
            <b>MaskObjects</b> in another pipeline to mask all images or objects in the
            group similarly.</li>
            </ul>
            <p>
            <b>References</b>
            <ul>
            <li>Selinummi J, Ruusuvuori P, Podolsky I, Ozinsky A, Gold E, et al. (2009)
            "Bright field microscopy as an alternative to whole cell fluorescence in
            automated analysis of macrophage images", <i>PLoS ONE</i> 4(10): e7497
            <a href="http://dx.doi.org/10.1371/journal.pone.0007497">(link)</a>.</li>
            </ul>
            </p> N/A globals N/A N/A self projection_image_name N/A N/A cps ImageNameProvider Name the output image ProjectionBlue doc 
            Enter the name for the projected image. provided_attributes N/A N/A cps AGGREGATE_IMAGE_ATTRIBUTE N/A cps AVAILABLE_ON_LAST_ATTRIBUTE True True N/A N/A self frequency N/A N/A cps Float Frequency 6.0 minval 1.0 doc N/A 
            <i>(Used only if %(P_POWER)s is selected as the projection method)</i><br>
            This setting controls the frequency at which the power
            is measured. A frequency of 2 will respond most strongly to
            pixels that alternate between dark and light in successive
            z-stack slices. A frequency of N will respond most strongly
            to pixels whose brightness cycle every N slices. N/A globals N/A settings N/A N/A self N/A N/A N/A N/A N/A self image_name N/A self projection_type N/A self projection_image_name N/A self frequency N/A visible_settings N/A N/A self N/A N/A N/A result N/A N/A self image_name N/A self projection_type N/A self projection_image_name N/A N/A N/A self projection_type P_POWER N/A N/A result N/A N/A self frequency N/A result N/A prepare_group N/A N/A self workspace grouping image_numbers N/A N/A N/A Reset the aggregate image at the start of group processing N/A N/A N/A len image_numbers 0 N/A N/A provider N/A ImageProvider N/A N/A self projection_image_name value N/A N/A self projection_type value N/A N/A self frequency value N/A N/A N/A provider save_state N/A N/A self get_dictionary N/A True N/A run N/A N/A self workspace N/A N/A N/A provider N/A N/A ImageProvider restore_from_state N/A N/A self get_dictionary N/A N/A N/A N/A N/A workspace image_set providers append provider N/A image N/A N/A N/A workspace image_set get_image N/A N/A self image_name value N/A pixels N/A image pixel_data N/A N/A N/A provider has_image N/A N/A N/A N/A provider set_image image N/A N/A N/A N/A provider accumulate_image image N/A N/A N/A provider save_state N/A N/A self get_dictionary N/A N/A self show_window N/A N/A N/A N/A workspace display_data pixels pixels N/A N/A N/A workspace display_data provider_pixels N/A N/A N/A provider provide_image N/A workspace image_set pixel_data N/A is_aggregation_module N/A N/A self N/A N/A N/A Return True because we aggregate over all images in a group N/A True N/A post_group N/A N/A self workspace grouping N/A N/A N/A Handle processing that takes place at the end of a group

        Add the provider to the workspace if not present. This could
        happen if the image set didn't reach this module.
         N/A image_set N/A workspace image_set N/A N/A N/A N/A self projection_image_name value N/A N/A image_set get_names N/A N/A provider N/A N/A ImageProvider restore_from_state N/A N/A self get_dictionary N/A N/A N/A N/A image_set providers append provider N/A display N/A N/A self workspace figure N/A N/A N/A pixels N/A N/A workspace display_data pixels N/A provider_pixels N/A N/A workspace display_data provider_pixels N/A N/A N/A figure set_subplots N/A 2 1 N/A N/A N/A provider_pixels ndim 3 N/A N/A N/A N/A figure subplot_imshow 0 0 pixels N/A N/A self image_name value N/A N/A N/A figure subplot_imshow 1 0 provider_pixels N/A N/A self projection_image_name value sharexy N/A N/A figure subplot 0 0 N/A N/A N/A N/A figure subplot_imshow_bw 0 0 pixels N/A N/A self image_name value N/A N/A N/A figure subplot_imshow_bw 1 0 provider_pixels N/A N/A self projection_image_name value sharexy N/A N/A figure subplot 0 0 N/A upgrade_settings N/A N/A self setting_values variable_revision_number module_name from_matlab N/A N/A N/A N/A from_matlab N/A module_name Average N/A N/A setting_values N/A N/A setting_values N/A 2 P_AVERAGE N/A from_matlab False N/A module_name N/A self module_name N/A variable_revision_number 1 N/A N/A from_matlab N/A module_name MakeProjection N/A variable_revision_number 3 N/A N/A setting_values N/A setting_values N/A 3 N/A from_matlab False N/A variable_revision_number 1 N/A N/A N/A from_matlab N/A variable_revision_number 1 N/A N/A setting_values N/A setting_values N/A 6 N/A N/A setting_values variable_revision_number from_matlab N/A N/A ImageProvider N/A N/A cpi AbstractImageProvider N/A N/A Provide the image after averaging but before dilation and smoothing __init__ N/A N/A self name how_to_accumulate frequency N/A 6 N/A N/A Construct using a parent provider that does the real work

        name - name of the image provided
         N/A N/A N/A N/A super ImageProvider self __init__ N/A N/A self __name name N/A N/A self frequency frequency N/A N/A self __image None N/A N/A self __how_to_accumulate how_to_accumulate N/A N/A self __image_count None N/A N/A self __cached_image None N/A N/A self __vsquared None N/A N/A self __vsum None N/A N/A self __power_image None N/A N/A self __power_mask None N/A N/A self __stack_number 0 N/A N/A self __bright_max None N/A N/A self __bright_min None N/A N/A self __norm0 None N/A N/A D_NAME name N/A D_FREQUENCY frequency N/A D_IMAGE image N/A D_HOW_TO_ACCUMULATE howtoaccumulate N/A D_IMAGE_COUNT imagecount N/A D_VSQUARED vsquared N/A D_VSUM vsum N/A D_POWER_IMAGE powerimage N/A D_POWER_MASK powermask N/A D_STACK_NUMBER stacknumber N/A D_BRIGHT_MAX brightmax N/A D_BRIGHT_MIN brightmin N/A D_NORM0 norm0 save_state N/A N/A self d N/A N/A N/A Save the provider state to a dictionary

        d - store state in this dictionary
         N/A N/A d N/A N/A self D_NAME N/A self __name N/A N/A d N/A N/A self D_FREQUENCY N/A self frequency N/A N/A d N/A N/A self D_IMAGE N/A self __image N/A N/A d N/A N/A self D_HOW_TO_ACCUMULATE N/A self __how_to_accumulate N/A N/A d N/A N/A self D_IMAGE_COUNT N/A self __image_count N/A N/A d N/A N/A self D_VSQUARED N/A self __vsquared N/A N/A d N/A N/A self D_VSUM N/A self __vsum N/A N/A d N/A N/A self D_POWER_IMAGE N/A self __power_image N/A N/A d N/A N/A self D_POWER_MASK N/A self __power_mask N/A N/A d N/A N/A self D_STACK_NUMBER N/A self __stack_number N/A N/A d N/A N/A self D_BRIGHT_MIN N/A self __bright_min N/A N/A d N/A N/A self D_BRIGHT_MAX N/A self __bright_max N/A N/A d N/A N/A self D_NORM0 N/A self __norm0 N/A restore_from_state N/A N/A d N/A N/A N/A Create a provider from the state stored in the dictionary

        d - dictionary from call to save_state

        returns a new ImageProvider built from the saved state
         N/A name N/A d N/A N/A ImageProvider D_NAME N/A frequency N/A d N/A N/A ImageProvider D_FREQUENCY N/A how_to_accumulate N/A d N/A N/A ImageProvider D_HOW_TO_ACCUMULATE N/A image_provider N/A ImageProvider name how_to_accumulate frequency N/A N/A image_provider __image N/A d N/A N/A ImageProvider D_IMAGE N/A N/A image_provider __image_count N/A d N/A N/A ImageProvider D_IMAGE_COUNT N/A N/A image_provider __vsquared N/A d N/A N/A ImageProvider D_VSQUARED N/A N/A image_provider __vsum N/A d N/A N/A ImageProvider D_VSUM N/A N/A image_provider __power_image N/A d N/A N/A ImageProvider D_POWER_IMAGE N/A N/A image_provider __power_mask N/A d N/A N/A ImageProvider D_POWER_MASK N/A N/A image_provider __stack_number N/A d N/A N/A ImageProvider D_STACK_NUMBER N/A N/A image_provider __bright_min N/A d N/A N/A ImageProvider D_BRIGHT_MIN N/A N/A image_provider __bright_max N/A d N/A N/A ImageProvider D_BRIGHT_MAX N/A N/A image_provider __norm0 N/A d N/A N/A ImageProvider D_NORM0 N/A image_provider N/A staticmethod reset N/A N/A self N/A N/A N/A Reset accumulator at start of groups N/A N/A self __image_count None N/A N/A self __image None N/A N/A self __cached_image None N/A N/A self __vsquared None N/A N/A self __vsum None N/A N/A self __power_image None N/A N/A self __power_mask None N/A N/A self __stack_number 0 N/A N/A self __bright_max None N/A N/A self __bright_min None N/A has_image N/A N/A self N/A N/A N/A N/A N/A self __image_count None N/A property count N/A N/A self N/A N/A N/A N/A self __image_count N/A property set_image N/A N/A self image N/A N/A N/A N/A self __cached_image None N/A N/A image has_mask N/A N/A N/A self __image_count N/A N/A N/A image mask astype int N/A N/A N/A self __image_count N/A N/A np ones N/A N/A N/A image pixel_data shape N/A 2 int N/A N/A N/A self __how_to_accumulate P_VARIANCE N/A N/A N/A self __vsum N/A N/A N/A image pixel_data copy N/A N/A N/A self __vsum N/A N/A N/A image mask 0 N/A N/A self __image_count N/A N/A N/A image mask astype int N/A N/A self __vsquared N/A N/A N/A N/A self __vsum astype N/A np float64 2.0 N/A N/A N/A N/A self __how_to_accumulate P_POWER N/A N/A N/A self __vsum N/A N/A N/A image pixel_data copy N/A N/A N/A self __vsum N/A N/A N/A image mask 0 N/A N/A self __image_count N/A N/A N/A image mask astype int N/A N/A self __power_mask N/A N/A N/A N/A N/A self __image_count astype N/A np complex128 copy N/A N/A self __power_image N/A N/A N/A N/A N/A image pixel_data astype N/A np complex128 copy N/A N/A self __stack_number 1 N/A N/A N/A N/A self __how_to_accumulate P_BRIGHTFIELD N/A N/A N/A self __bright_max N/A N/A N/A image pixel_data copy N/A N/A self __bright_min N/A N/A N/A image pixel_data copy N/A N/A self __norm0 N/A N/A np mean N/A image pixel_data N/A N/A N/A N/A self __how_to_accumulate P_MASK N/A N/A N/A self __image N/A image mask N/A N/A N/A self __image N/A N/A N/A image pixel_data copy N/A N/A image has_mask N/A N/A nan_value N/A N/A N/A self __how_to_accumulate P_MINIMUM 1 0 N/A N/A N/A self __image N/A N/A N/A image mask nan_value N/A accumulate_image N/A N/A self image N/A N/A N/A N/A self __cached_image None N/A N/A image has_mask N/A N/A N/A self __image_count N/A N/A N/A image mask astype int N/A N/A N/A self __image_count 1 N/A N/A N/A self __how_to_accumulate N/A P_AVERAGE P_SUM N/A N/A N/A image has_mask N/A N/A N/A N/A self __image N/A N/A image mask N/A N/A image pixel_data N/A N/A image mask N/A N/A N/A self __image N/A image pixel_data N/A N/A N/A N/A self __how_to_accumulate P_MAXIMUM N/A N/A N/A image has_mask N/A N/A N/A N/A self __image N/A N/A image mask N/A N/A np maximum N/A N/A self __image N/A N/A image mask N/A N/A image pixel_data N/A N/A image mask N/A N/A N/A self __image N/A N/A np maximum N/A image pixel_data N/A self __image N/A N/A N/A N/A self __how_to_accumulate P_MINIMUM N/A N/A N/A image has_mask N/A N/A N/A N/A self __image N/A N/A image mask N/A N/A np minimum N/A N/A self __image N/A N/A image mask N/A N/A image pixel_data N/A N/A image mask N/A N/A N/A self __image N/A N/A np minimum N/A image pixel_data N/A self __image N/A N/A N/A N/A self __how_to_accumulate P_VARIANCE N/A N/A mask N/A image mask N/A N/A N/A self __vsum N/A mask N/A N/A image pixel_data N/A mask N/A N/A N/A self __vsquared N/A mask N/A N/A N/A N/A N/A image pixel_data N/A mask astype N/A np float64 2 N/A N/A N/A N/A self __how_to_accumulate P_POWER N/A N/A multiplier N/A N/A np exp N/A N/A N/A 2j N/A np pi N/A float N/A self __stack_number N/A self frequency N/A N/A self __stack_number 1 N/A mask N/A image mask N/A N/A N/A self __vsum N/A mask N/A N/A image pixel_data N/A mask N/A N/A N/A self __power_image N/A mask N/A multiplier N/A N/A image pixel_data N/A mask N/A N/A N/A self __power_mask N/A mask multiplier N/A N/A N/A N/A self __how_to_accumulate P_BRIGHTFIELD N/A N/A mask N/A image mask N/A norm N/A N/A np mean N/A image pixel_data N/A pixel_data N/A N/A N/A image pixel_data N/A self __norm0 norm N/A max_mask N/A N/A N/A self __bright_max pixel_data mask N/A min_mask N/A N/A N/A self __bright_min pixel_data mask N/A N/A N/A self __bright_min N/A min_mask N/A pixel_data N/A min_mask N/A N/A N/A self __bright_max N/A max_mask N/A pixel_data N/A max_mask N/A N/A N/A self __bright_min N/A max_mask N/A N/A self __bright_max N/A max_mask N/A N/A N/A N/A self __how_to_accumulate P_MASK N/A N/A N/A self __image N/A N/A self __image N/A image mask N/A N/A N/A NotImplementedError N/A No such accumulation method: %s N/A self __how_to_accumulate N/A provide_image N/A N/A self image_set N/A N/A N/A image_count N/A self __image_count N/A mask_2d N/A image_count 0 N/A N/A N/A self __how_to_accumulate P_VARIANCE N/A N/A ndim_image N/A self __vsquared N/A N/A N/A N/A self __how_to_accumulate P_POWER N/A N/A ndim_image N/A self __power_image N/A N/A N/A N/A self __how_to_accumulate P_BRIGHTFIELD N/A N/A ndim_image N/A self __bright_max N/A N/A ndim_image N/A self __image N/A N/A N/A ndim_image ndim 3 N/A N/A image_count N/A N/A np dstack N/A N/A image_count N/A N/A ndim_image shape N/A 2 N/A mask N/A image_count 0 N/A N/A N/A self __cached_image None N/A N/A N/A self __cached_image N/A N/A N/A self __how_to_accumulate P_AVERAGE N/A N/A cached_image N/A N/A self __image image_count N/A N/A N/A N/A self __how_to_accumulate P_VARIANCE N/A N/A cached_image N/A N/A np zeros N/A N/A self __vsquared shape N/A np float32 N/A N/A cached_image N/A mask N/A N/A N/A self __vsquared N/A mask N/A image_count N/A mask N/A N/A cached_image N/A mask N/A N/A N/A N/A self __vsum N/A mask 2 N/A N/A image_count N/A mask 2 N/A N/A N/A N/A self __how_to_accumulate P_POWER N/A N/A cached_image N/A N/A np zeros N/A image_count shape N/A np complex128 N/A N/A cached_image N/A mask N/A N/A self __power_image N/A mask N/A N/A cached_image N/A mask N/A N/A N/A N/A self __vsum N/A mask N/A N/A self __power_mask N/A mask N/A image_count N/A mask N/A cached_image N/A N/A N/A N/A cached_image N/A N/A np conj cached_image real astype N/A np float32 N/A N/A N/A N/A self __how_to_accumulate P_BRIGHTFIELD N/A N/A cached_image N/A N/A np zeros N/A image_count shape N/A np float32 N/A N/A cached_image N/A mask N/A N/A N/A self __bright_max N/A mask N/A N/A self __bright_min N/A mask N/A N/A N/A N/A N/A self __how_to_accumulate P_MINIMUM N/A N/A np any N/A mask N/A N/A cached_image N/A N/A N/A self __image copy N/A N/A cached_image N/A N/A mask 0 N/A N/A cached_image N/A self __image N/A N/A cached_image N/A N/A mask 0 N/A N/A N/A N/A np all mask N/A N/A self __how_to_accumulate P_MASK N/A N/A N/A self __cached_image N/A N/A cpi Image cached_image N/A N/A N/A self __cached_image N/A N/A cpi Image cached_image mask mask_2d N/A N/A self __cached_image N/A get_name N/A N/A self N/A N/A N/A N/A self __name N/A release_memory N/A N/A self N/A N/A N/A Don't discard the image at end of image set N/A N/A N/A