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Deprecate broken ImagingRetinotopy module (#1813)
* Update retinotopy.py * Remove references to retinotopy module * Update schema * Fix test * Updated changelog * Update schema submodule * Update test_retinotopy.py * Update retinotopy.py * Update test_retinotopy.py * Update retinotopy.py * Update test_retinotopy.py * Update retinotopy.py * Update test_retinotopy.py * RuntimeError -> ImportError * Update schema * Revert "Update schema" This reverts commit 08f3a88. * Update schema
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Submodule nwb-schema
updated
4 files
| +1 −1 | Legal.txt | |
| +2 −2 | README.rst | |
| +1 −1 | hdmf-common-schema | |
| +1 −1 | license.txt |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,145 +1,149 @@ | ||
| import warnings | ||
| from collections.abc import Iterable | ||
|
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| from hdmf.utils import docval, popargs, get_docval | ||
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| from . import register_class, CORE_NAMESPACE | ||
| from .core import NWBDataInterface, NWBData | ||
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| class RetinotopyImage(NWBData): | ||
| """Gray-scale anatomical image of cortical surface. Array structure: [rows][columns] | ||
| """ | ||
|
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| __nwbfields__ = ('bits_per_pixel', | ||
| 'dimension', | ||
| 'format', | ||
| 'field_of_view') | ||
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| @docval({'name': 'name', 'type': str, 'doc': 'Name of this retinotopy image'}, | ||
| {'name': 'data', 'type': Iterable, 'doc': 'Data field.'}, | ||
| {'name': 'bits_per_pixel', 'type': int, | ||
| 'doc': 'Number of bits used to represent each value. This is necessary to determine maximum ' | ||
| '(white) pixel value.'}, | ||
| {'name': 'dimension', 'type': Iterable, 'shape': (2, ), 'doc': 'Number of rows and columns in the image.'}, | ||
| {'name': 'format', 'type': Iterable, 'doc': 'Format of image. Right now only "raw" supported.'}, | ||
| {'name': 'field_of_view', 'type': Iterable, 'shape': (2, ), 'doc': 'Size of viewing area, in meters.'}) | ||
| def __init__(self, **kwargs): | ||
| bits_per_pixel, dimension, format, field_of_view = popargs( | ||
| 'bits_per_pixel', 'dimension', 'format', 'field_of_view', kwargs) | ||
| super().__init__(**kwargs) | ||
| self.bits_per_pixel = bits_per_pixel | ||
| self.dimension = dimension | ||
| self.format = format | ||
| self.field_of_view = field_of_view | ||
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| class FocalDepthImage(RetinotopyImage): | ||
| """Gray-scale image taken with same settings/parameters (e.g., focal depth, | ||
| wavelength) as data collection. Array format: [rows][columns]. | ||
| """ | ||
|
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| __nwbfields__ = ('focal_depth', ) | ||
|
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| @docval(*get_docval(RetinotopyImage.__init__), | ||
| {'name': 'focal_depth', 'type': float, 'doc': 'Focal depth offset, in meters.'}) | ||
| def __init__(self, **kwargs): | ||
| focal_depth = popargs('focal_depth', kwargs) | ||
| super().__init__(**kwargs) | ||
| self.focal_depth = focal_depth | ||
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|
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| class RetinotopyMap(NWBData): | ||
| """Abstract two-dimensional map of responses to stimuli along a single response axis (e.g., altitude) | ||
| """ | ||
|
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| __nwbfields__ = ('field_of_view', | ||
| 'dimension') | ||
|
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| @docval({'name': 'name', 'type': str, 'doc': 'the name of this axis map'}, | ||
| {'name': 'data', 'type': Iterable, 'shape': (None, None), 'doc': 'data field.'}, | ||
| {'name': 'field_of_view', 'type': Iterable, 'shape': (2, ), 'doc': 'Size of viewing area, in meters.'}, | ||
| {'name': 'dimension', 'type': Iterable, 'shape': (2, ), | ||
| 'doc': 'Number of rows and columns in the image'}) | ||
| def __init__(self, **kwargs): | ||
| field_of_view, dimension = popargs('field_of_view', 'dimension', kwargs) | ||
| super().__init__(**kwargs) | ||
| self.field_of_view = field_of_view | ||
| self.dimension = dimension | ||
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|
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| class AxisMap(RetinotopyMap): | ||
| """Abstract two-dimensional map of responses to stimuli along a single response axis (e.g., altitude) with unit | ||
| """ | ||
|
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| __nwbfields__ = ('unit', ) | ||
|
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| @docval(*get_docval(RetinotopyMap.__init__, 'name', 'data', 'field_of_view'), | ||
| {'name': 'unit', 'type': str, 'doc': 'Unit that axis data is stored in (e.g., degrees)'}, | ||
| *get_docval(RetinotopyMap.__init__, 'dimension')) | ||
| def __init__(self, **kwargs): | ||
| unit = popargs('unit', kwargs) | ||
| super().__init__(**kwargs) | ||
| self.unit = unit | ||
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| @register_class('ImagingRetinotopy', CORE_NAMESPACE) | ||
| class ImagingRetinotopy(NWBDataInterface): | ||
| """ | ||
| Intrinsic signal optical imaging or widefield imaging for measuring retinotopy. Stores orthogonal | ||
| maps (e.g., altitude/azimuth; radius/theta) of responses to specific stimuli and a combined | ||
| polarity map from which to identify visual areas. | ||
| This group does not store the raw responses imaged during retinotopic mapping or the | ||
| stimuli presented, but rather the resulting phase and power maps after applying a Fourier | ||
| transform on the averaged responses. | ||
| Note: for data consistency, all images and arrays are stored in the format [row][column] and | ||
| [row, col], which equates to [y][x]. Field of view and dimension arrays may appear backward | ||
| (i.e., y before x). | ||
| """ | ||
|
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| __nwbfields__ = ({'name': 'sign_map', 'child': True}, | ||
| {'name': 'axis_1_phase_map', 'child': True}, | ||
| {'name': 'axis_1_power_map', 'child': True}, | ||
| {'name': 'axis_2_phase_map', 'child': True}, | ||
| {'name': 'axis_2_power_map', 'child': True}, | ||
| {'name': 'focal_depth_image', 'child': True}, | ||
| {'name': 'vasculature_image', 'child': True}, | ||
| 'axis_descriptions') | ||
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| @docval({'name': 'sign_map', 'type': RetinotopyMap, | ||
| 'doc': 'Sine of the angle between the direction of the gradient in axis_1 and axis_2.'}, | ||
| {'name': 'axis_1_phase_map', 'type': AxisMap, | ||
| 'doc': 'Phase response to stimulus on the first measured axis.'}, | ||
| {'name': 'axis_1_power_map', 'type': AxisMap, | ||
| 'doc': 'Power response on the first measured axis. Response is scaled so 0.0 is no power in ' | ||
| 'the response and 1.0 is maximum relative power.'}, | ||
| {'name': 'axis_2_phase_map', 'type': AxisMap, | ||
| 'doc': 'Phase response to stimulus on the second measured axis.'}, | ||
| {'name': 'axis_2_power_map', 'type': AxisMap, | ||
| 'doc': 'Power response on the second measured axis. Response is scaled so 0.0 is no ' | ||
| 'power in the response and 1.0 is maximum relative power.'}, | ||
| {'name': 'axis_descriptions', 'type': Iterable, 'shape': (2, ), | ||
| 'doc': 'Two-element array describing the contents of the two response axis fields. ' | ||
| 'Description should be something like ["altitude", "azimuth"] or ["radius", "theta"].'}, | ||
| {'name': 'focal_depth_image', 'type': FocalDepthImage, | ||
| 'doc': 'Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) ' | ||
| 'as data collection. Array format: [rows][columns].'}, | ||
| {'name': 'vasculature_image', 'type': RetinotopyImage, | ||
| 'doc': 'Gray-scale anatomical image of cortical surface. Array structure: [rows][columns].'}, | ||
| {'name': 'name', 'type': str, 'doc': 'the name of this container', 'default': 'ImagingRetinotopy'}) | ||
| def __init__(self, **kwargs): | ||
| axis_1_phase_map, axis_1_power_map, axis_2_phase_map, axis_2_power_map, axis_descriptions, \ | ||
| focal_depth_image, sign_map, vasculature_image = popargs( | ||
| 'axis_1_phase_map', 'axis_1_power_map', 'axis_2_phase_map', 'axis_2_power_map', | ||
| 'axis_descriptions', 'focal_depth_image', 'sign_map', 'vasculature_image', kwargs) | ||
| super().__init__(**kwargs) | ||
| warnings.warn("The ImagingRetinotopy class currently cannot be written to or read from a file. " | ||
| "This is a known bug and will be fixed in a future release of PyNWB.") | ||
| self.axis_1_phase_map = axis_1_phase_map | ||
| self.axis_1_power_map = axis_1_power_map | ||
| self.axis_2_phase_map = axis_2_phase_map | ||
| self.axis_2_power_map = axis_2_power_map | ||
| self.axis_descriptions = axis_descriptions | ||
| self.focal_depth_image = focal_depth_image | ||
| self.sign_map = sign_map | ||
| self.vasculature_image = vasculature_image | ||
| raise ImportError( | ||
| "The pynwb.retinotopy module is deprecated. If you are interested in using these neurodata types, " | ||
| "please create an issue on https://github.com/NeurodataWithoutBorders/nwb-schema/issues." | ||
| ) | ||
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| # import warnings | ||
| # from collections.abc import Iterable | ||
|
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| # from hdmf.utils import docval, popargs, get_docval | ||
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| # from . import register_class, CORE_NAMESPACE | ||
| # from .core import NWBDataInterface, NWBData | ||
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| # class RetinotopyImage(NWBData): | ||
| # """Gray-scale anatomical image of cortical surface. Array structure: [rows][columns] | ||
| # """ | ||
|
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| # __nwbfields__ = ('bits_per_pixel', | ||
| # 'dimension', | ||
| # 'format', | ||
| # 'field_of_view') | ||
|
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| # @docval({'name': 'name', 'type': str, 'doc': 'Name of this retinotopy image'}, | ||
| # {'name': 'data', 'type': Iterable, 'doc': 'Data field.'}, | ||
| # {'name': 'bits_per_pixel', 'type': int, | ||
| # 'doc': 'Number of bits used to represent each value. This is necessary to determine maximum ' | ||
| # '(white) pixel value.'}, | ||
| # {'name': 'dimension', 'type': Iterable, 'shape': (2, ), | ||
| # 'doc': 'Number of rows and columns in the image.'}, | ||
| # {'name': 'format', 'type': Iterable, 'doc': 'Format of image. Right now only "raw" supported.'}, | ||
| # {'name': 'field_of_view', 'type': Iterable, 'shape': (2, ), 'doc': 'Size of viewing area, in meters.'}) | ||
| # def __init__(self, **kwargs): | ||
| # bits_per_pixel, dimension, format, field_of_view = popargs( | ||
| # 'bits_per_pixel', 'dimension', 'format', 'field_of_view', kwargs) | ||
| # super().__init__(**kwargs) | ||
| # self.bits_per_pixel = bits_per_pixel | ||
| # self.dimension = dimension | ||
| # self.format = format | ||
| # self.field_of_view = field_of_view | ||
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| # class FocalDepthImage(RetinotopyImage): | ||
| # """Gray-scale image taken with same settings/parameters (e.g., focal depth, | ||
| # wavelength) as data collection. Array format: [rows][columns]. | ||
| # """ | ||
|
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| # __nwbfields__ = ('focal_depth', ) | ||
|
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| # @docval(*get_docval(RetinotopyImage.__init__), | ||
| # {'name': 'focal_depth', 'type': float, 'doc': 'Focal depth offset, in meters.'}) | ||
| # def __init__(self, **kwargs): | ||
| # focal_depth = popargs('focal_depth', kwargs) | ||
| # super().__init__(**kwargs) | ||
| # self.focal_depth = focal_depth | ||
|
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|
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| # class RetinotopyMap(NWBData): | ||
| # """Abstract two-dimensional map of responses to stimuli along a single response axis (e.g., altitude) | ||
| # """ | ||
|
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| # __nwbfields__ = ('field_of_view', | ||
| # 'dimension') | ||
|
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| # @docval({'name': 'name', 'type': str, 'doc': 'the name of this axis map'}, | ||
| # {'name': 'data', 'type': Iterable, 'shape': (None, None), 'doc': 'data field.'}, | ||
| # {'name': 'field_of_view', 'type': Iterable, 'shape': (2, ), 'doc': 'Size of viewing area, in meters.'}, | ||
| # {'name': 'dimension', 'type': Iterable, 'shape': (2, ), | ||
| # 'doc': 'Number of rows and columns in the image'}) | ||
| # def __init__(self, **kwargs): | ||
| # field_of_view, dimension = popargs('field_of_view', 'dimension', kwargs) | ||
| # super().__init__(**kwargs) | ||
| # self.field_of_view = field_of_view | ||
| # self.dimension = dimension | ||
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|
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| # class AxisMap(RetinotopyMap): | ||
| # """Abstract two-dimensional map of responses to stimuli along a single response axis (e.g., altitude) with unit | ||
| # """ | ||
|
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| # __nwbfields__ = ('unit', ) | ||
|
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| # @docval(*get_docval(RetinotopyMap.__init__, 'name', 'data', 'field_of_view'), | ||
| # {'name': 'unit', 'type': str, 'doc': 'Unit that axis data is stored in (e.g., degrees)'}, | ||
| # *get_docval(RetinotopyMap.__init__, 'dimension')) | ||
| # def __init__(self, **kwargs): | ||
| # unit = popargs('unit', kwargs) | ||
| # super().__init__(**kwargs) | ||
| # self.unit = unit | ||
|
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|
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| # @register_class('ImagingRetinotopy', CORE_NAMESPACE) | ||
| # class ImagingRetinotopy(NWBDataInterface): | ||
| # """ | ||
| # Intrinsic signal optical imaging or widefield imaging for measuring retinotopy. Stores orthogonal | ||
| # maps (e.g., altitude/azimuth; radius/theta) of responses to specific stimuli and a combined | ||
| # polarity map from which to identify visual areas. | ||
| # This group does not store the raw responses imaged during retinotopic mapping or the | ||
| # stimuli presented, but rather the resulting phase and power maps after applying a Fourier | ||
| # transform on the averaged responses. | ||
| # Note: for data consistency, all images and arrays are stored in the format [row][column] and | ||
| # [row, col], which equates to [y][x]. Field of view and dimension arrays may appear backward | ||
| # (i.e., y before x). | ||
| # """ | ||
|
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| # __nwbfields__ = ({'name': 'sign_map', 'child': True}, | ||
| # {'name': 'axis_1_phase_map', 'child': True}, | ||
| # {'name': 'axis_1_power_map', 'child': True}, | ||
| # {'name': 'axis_2_phase_map', 'child': True}, | ||
| # {'name': 'axis_2_power_map', 'child': True}, | ||
| # {'name': 'focal_depth_image', 'child': True}, | ||
| # {'name': 'vasculature_image', 'child': True}, | ||
| # 'axis_descriptions') | ||
|
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| # @docval({'name': 'sign_map', 'type': RetinotopyMap, | ||
| # 'doc': 'Sine of the angle between the direction of the gradient in axis_1 and axis_2.'}, | ||
| # {'name': 'axis_1_phase_map', 'type': AxisMap, | ||
| # 'doc': 'Phase response to stimulus on the first measured axis.'}, | ||
| # {'name': 'axis_1_power_map', 'type': AxisMap, | ||
| # 'doc': 'Power response on the first measured axis. Response is scaled so 0.0 is no power in ' | ||
| # 'the response and 1.0 is maximum relative power.'}, | ||
| # {'name': 'axis_2_phase_map', 'type': AxisMap, | ||
| # 'doc': 'Phase response to stimulus on the second measured axis.'}, | ||
| # {'name': 'axis_2_power_map', 'type': AxisMap, | ||
| # 'doc': 'Power response on the second measured axis. Response is scaled so 0.0 is no ' | ||
| # 'power in the response and 1.0 is maximum relative power.'}, | ||
| # {'name': 'axis_descriptions', 'type': Iterable, 'shape': (2, ), | ||
| # 'doc': 'Two-element array describing the contents of the two response axis fields. ' | ||
| # 'Description should be something like ["altitude", "azimuth"] or ["radius", "theta"].'}, | ||
| # {'name': 'focal_depth_image', 'type': FocalDepthImage, | ||
| # 'doc': 'Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) ' | ||
| # 'as data collection. Array format: [rows][columns].'}, | ||
| # {'name': 'vasculature_image', 'type': RetinotopyImage, | ||
| # 'doc': 'Gray-scale anatomical image of cortical surface. Array structure: [rows][columns].'}, | ||
| # {'name': 'name', 'type': str, 'doc': 'the name of this container', 'default': 'ImagingRetinotopy'}) | ||
| # def __init__(self, **kwargs): | ||
| # axis_1_phase_map, axis_1_power_map, axis_2_phase_map, axis_2_power_map, axis_descriptions, \ | ||
| # focal_depth_image, sign_map, vasculature_image = popargs( | ||
| # 'axis_1_phase_map', 'axis_1_power_map', 'axis_2_phase_map', 'axis_2_power_map', | ||
| # 'axis_descriptions', 'focal_depth_image', 'sign_map', 'vasculature_image', kwargs) | ||
| # super().__init__(**kwargs) | ||
| # self.axis_1_phase_map = axis_1_phase_map | ||
| # self.axis_1_power_map = axis_1_power_map | ||
| # self.axis_2_phase_map = axis_2_phase_map | ||
| # self.axis_2_power_map = axis_2_power_map | ||
| # self.axis_descriptions = axis_descriptions | ||
| # self.focal_depth_image = focal_depth_image | ||
| # self.sign_map = sign_map | ||
| # self.vasculature_image = vasculature_image |
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