The final product of the **Images** module is a file list in which any
files that are not intended for further processing have been removed,
whether manually or using filtering. This list will be used when
collecting metadata (if desired) and when assembling the image sets in
NamesAndTypes. The list can be filtered further in NamesAndTypes to
specify, for example, that a subset of these images represents a
particular wavelength.
.. _here: http://www.openmicroscopy.org/site/support/bio-formats5/supported-formats.html
.. _“lossy”: http://www.techterms.com/definition/lossy
.. _“lossless”: http://www.techterms.com/definition/lossless
""".format(
**{
"IMG_PANEL_BLANK":
_help.__image_resource('Images_FilelistPanel_Blank.png'),
"IMG_PANEL_FILLED":
_help.__image_resource('Images_FilelistPanel_Filled.png')
})
FILTER_CHOICE_NONE = "No filtering"
FILTER_CHOICE_IMAGES = "Images only"
FILTER_CHOICE_CUSTOM = "Custom"
FILTER_CHOICE_ALL = [
FILTER_CHOICE_NONE, FILTER_CHOICE_IMAGES, FILTER_CHOICE_CUSTOM
]
FILTER_DEFAULT = 'and (extension does isimage) (directory doesnot containregexp "[\\\\\\\\/]\\\\.")'
class Images(cpm.Module):
- *Group\_Index:* The index of each imaget set within each grouping, as
defined by the *Group\_Number*. These are written to the per-image
table.
Technical notes
^^^^^^^^^^^^^^^
To perform grouping, only one analysis worker (i.e., copy of
CellProfiler) will be allocated to handle each group. This means that
you may have multiple workers created (as set under the Preferences),
but only a subset of them may actually be active, depending on the
number of groups you have.
""".format(
**{
"GROUPS_DISPLAY_TABLE":
_help.__image_resource('Groups_ExampleDisplayTable.png')
})
class Groups(cpm.Module):
variable_revision_number = 2
module_name = "Groups"
category = "File Processing"
IDX_GROUPING_METADATA_COUNT = 1
def create_settings(self):
self.pipeline = None
self.metadata_keys = {}
module_explanation = [
tracking of objects”, Proceedings from XV Brazilian Symposium on
Computer Graphics and Image Processing, 2002. `(pdf)`_
- Principles of Digital Image Processing: Core Algorithms
(Undergraduate Topics in Computer Science): `Section 2.4.3 -
Statistical shape properties`_
- Chrystal P (1885), “On the problem to construct the minimum circle
enclosing n given points in a plane”, *Proceedings of the Edinburgh
Mathematical Society*, vol 3, p. 30
.. _(pdf): http://sibgrapi.sid.inpe.br/col/sid.inpe.br/banon/2002/10.23.11.34/doc/35.pdf
.. _Section 2.4.3 - Statistical shape properties: http://www.scribd.com/doc/58004056/Principles-of-Digital-Image-Processing#page=49
.. |MOSS_image0| image:: {ECCENTRICITY_ICON}
""".format(
**{
"ECCENTRICITY_ICON":
_help.__image_resource("MeasureObjectSizeShape_Eccentricity.png")
})
"""The category of the per-object measurements made by this module"""
AREA_SHAPE = 'AreaShape'
"""Calculate Zernike features for N,M where N=0 through ZERNIKE_N"""
ZERNIKE_N = 9
F_AREA = "Area"
F_ECCENTRICITY = 'Eccentricity'
F_SOLIDITY = 'Solidity'
F_EXTENT = 'Extent'
F_CENTER_X = 'Center_X'
F_CENTER_Y = 'Center_Y'
F_CENTER_Z = 'Center_Z'
F_EULER_NUMBER = 'EulerNumber'
F_PERIMETER = 'Perimeter'
combinations of the metadata tags specified. These are written to the
per-image table.
- *Group\_Index:* The index of each image set within each grouping, as
defined by the *Group\_Number*. These are written to the per-image
table.
Technical notes
^^^^^^^^^^^^^^^
To perform grouping, only one analysis worker (i.e., copy of
CellProfiler) will be allocated to handle each group. This means that
you may have multiple workers created (as set under the Preferences),
but only a subset of them may actually be active, depending on the
number of groups you have.
""".format(**{
"GROUPS_DISPLAY_TABLE": _help.__image_resource('Groups_ExampleDisplayTable.png')
})
class Groups(cpm.Module):
variable_revision_number = 2
module_name = "Groups"
category = "File Processing"
IDX_GROUPING_METADATA_COUNT = 1
def create_settings(self):
self.pipeline = None
self.metadata_keys = {}
module_explanation = [
"The %s module optionally allows you to split your list of images into image subsets" % self.module_name,
What do I get as output?
^^^^^^^^^^^^^^^^^^^^^^^^
The final product of the **Images** module is a file list in which any
files that are not intended for further processing have been removed,
whether manually or using filtering. This list will be used when
collecting metadata (if desired) and when assembling the image sets in
NamesAndTypes. The list can be filtered further in NamesAndTypes to
specify, for example, that a subset of these images represents a
particular wavelength.
.. _here: http://www.openmicroscopy.org/site/support/bio-formats5/supported-formats.html
.. _“lossy”: http://www.techterms.com/definition/lossy
.. _“lossless”: http://www.techterms.com/definition/lossless
""".format(**{
"IMG_PANEL_BLANK": _help.__image_resource('Images_FilelistPanel_Blank.png'),
"IMG_PANEL_FILLED": _help.__image_resource('Images_FilelistPanel_Filled.png')
})
FILTER_CHOICE_NONE = "No filtering"
FILTER_CHOICE_IMAGES = "Images only"
FILTER_CHOICE_CUSTOM = "Custom"
FILTER_CHOICE_ALL = [FILTER_CHOICE_NONE, FILTER_CHOICE_IMAGES,
FILTER_CHOICE_CUSTOM]
FILTER_DEFAULT = 'and (extension does isimage) (directory doesnot containregexp "[\\\\\\\\/]\\\\.")'
class Images(cpm.Module):
variable_revision_number = 2
- Rocha L, Velho L, Carvalho PCP, “Image moments-based structuring and
tracking of objects”, Proceedings from XV Brazilian Symposium on
Computer Graphics and Image Processing, 2002. `(pdf)`_
- Principles of Digital Image Processing: Core Algorithms
(Undergraduate Topics in Computer Science): `Section 2.4.3 -
Statistical shape properties`_
- Chrystal P (1885), “On the problem to construct the minimum circle
enclosing n given points in a plane”, *Proceedings of the Edinburgh
Mathematical Society*, vol 3, p. 30
.. _(pdf): http://sibgrapi.sid.inpe.br/col/sid.inpe.br/banon/2002/10.23.11.34/doc/35.pdf
.. _Section 2.4.3 - Statistical shape properties: http://www.scribd.com/doc/58004056/Principles-of-Digital-Image-Processing#page=49
.. |MOSS_image0| image:: {ECCENTRICITY_ICON}
""".format(**{
"ECCENTRICITY_ICON": _help.__image_resource("MeasureObjectSizeShape_Eccentricity.png")
})
"""The category of the per-object measurements made by this module"""
AREA_SHAPE = 'AreaShape'
"""Calculate Zernike features for N,M where N=0 through ZERNIKE_N"""
ZERNIKE_N = 9
F_AREA = "Area"
F_ECCENTRICITY = 'Eccentricity'
F_SOLIDITY = 'Solidity'
F_EXTENT = 'Extent'
F_CENTER_X = 'Center_X'
F_CENTER_Y = 'Center_Y'
F_CENTER_Z = 'Center_Z'