Moved cdl.core.computation to cdl.computation

Author: PierreRaybaut

CHANGELOG.md

@@ -337,7 +337,7 @@ for future and past milestones.
     parameters for a new signal
   * Added `edit_new_image_parameters` method for showing a dialog box to edit
     parameters for a new image (updated the *cdl_testdata.py* plugin accordingly)
-* Signal and image computations API (`cdl.core.computations`):
+* Signal and image computations API (`cdl.computations`):
   * Added wrappers for signal and image 1 -> 1 computations
   * These wrappers aim at simplifying the creation of a basic computation function
     operating on DataLab's native objects (`SignalObj` and `ImageObj`) from a

cdl/algorithms/__init__.py

@@ -9,7 +9,7 @@
 .. seealso::
 
     The :mod:`cdl.algorithms` package is the main entry point for the DataLab
-    algorithms when manipulating NumPy arrays. See the :mod:`cdl.core.computation`
+    algorithms when manipulating NumPy arrays. See the :mod:`cdl.computation`
     package for algorithms that operate directly on DataLab objects (i.e.
     :class:`cdl.obj.SignalObj` and :class:`cdl.obj.ImageObj`).
 

cdl/core/computation/__init__.py cdl/computation/__init__.pycdl/core/computation/__init__.py renamed to cdl/computation/__init__.py

@@ -1,5 +1,5 @@
 """
-Computation (:mod:`cdl.core.computation`)
+Computation (:mod:`cdl.computation`)
 -----------------------------------------
 
 This package contains the computation functions used by the DataLab project.
@@ -9,7 +9,7 @@
 
 .. seealso::
 
-    The :mod:`cdl.core.computation` package is the main entry point for the DataLab
+    The :mod:`cdl.computation` package is the main entry point for the DataLab
     computation functions when manipulating DataLab objects.
     See the :mod:`cdl.algorithms` package for algorithms that operate directly on
     NumPy arrays.
@@ -31,20 +31,20 @@
 The computation modules are organized in subpackages according to their purpose.
 The following subpackages are available:
 
-- :mod:`cdl.core.computation.base`: Common processing features
-- :mod:`cdl.core.computation.signal`: Signal processing features
-- :mod:`cdl.core.computation.image`: Image processing features
+- :mod:`cdl.computation.base`: Common processing features
+- :mod:`cdl.computation.signal`: Signal processing features
+- :mod:`cdl.computation.image`: Image processing features
 
 Common processing features
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: cdl.core.computation.base
+.. automodule:: cdl.computation.base
    :members:
 
 Signal processing features
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: cdl.core.computation.signal
+.. automodule:: cdl.computation.signal
    :members:
 
 Image processing features
@@ -53,35 +53,35 @@
 Base image processing features
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. automodule:: cdl.core.computation.image
+.. automodule:: cdl.computation.image
    :members:
 
 Exposure correction features
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. automodule:: cdl.core.computation.image.exposure
+.. automodule:: cdl.computation.image.exposure
     :members:
 
 Restoration features
 ~~~~~~~~~~~~~~~~~~~~
 
-.. automodule:: cdl.core.computation.image.restoration
+.. automodule:: cdl.computation.image.restoration
     :members:
 
 Morphological features
 ~~~~~~~~~~~~~~~~~~~~~~
 
-.. automodule:: cdl.core.computation.image.morphology
+.. automodule:: cdl.computation.image.morphology
     :members:
 
 Edge detection features
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-.. automodule:: cdl.core.computation.image.edges
+.. automodule:: cdl.computation.image.edges
 
 Detection features
 ~~~~~~~~~~~~~~~~~~
 
-.. automodule:: cdl.core.computation.image.detection
+.. automodule:: cdl.computation.image.detection
     :members:
 """

cdl/core/computation/base.py cdl/computation/base.pycdl/core/computation/base.py renamed to cdl/computation/base.py

@@ -1,14 +1,14 @@
 # Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
 
 """
-.. Common computation objects (see parent package :mod:`cdl.core.computation`)
+.. Common computation objects (see parent package :mod:`cdl.computation`)
 """
 
 # pylint: disable=invalid-name  # Allows short reference names like x, y, ...
 
 # Note:
 # ----
-# All dataset classes must also be imported in the cdl.core.computation.param module.
+# All dataset classes must also be imported in the cdl.computation.param module.
 
 from __future__ import annotations
 
@@ -18,14 +18,12 @@
 import numpy as np
 
 from cdl.config import _
-from cdl.core.model.base import ResultProperties
-from cdl.core.model.signal import create_signal
+from cdl.obj import ResultProperties, create_signal
 
 if TYPE_CHECKING:
     from typing import Callable
 
-    from cdl.core.model.image import ImageObj
-    from cdl.core.model.signal import SignalObj
+    from cdl.obj import ImageObj, SignalObj
 
 
 class GaussianParam(gds.DataSet):

cdl/core/computation/image/__init__.py cdl/computation/image/__init__.pycdl/core/computation/image/__init__.py renamed to cdl/computation/image/__init__.py

@@ -1,7 +1,7 @@
 # Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
 
 """
-.. Image computation objects (see parent package :mod:`cdl.core.computation`)
+.. Image computation objects (see parent package :mod:`cdl.computation`)
 """
 
 # pylint: disable=invalid-name  # Allows short reference names like x, y, ...
@@ -25,8 +25,7 @@
 from skimage import filters
 
 import cdl.algorithms.image as alg
-from cdl.config import _
-from cdl.core.computation.base import (
+from cdl.computation.base import (
     ClipParam,
     ConstantOperationParam,
     FFTParam,
@@ -41,9 +40,17 @@
     dst_n1n,
     new_signal_result,
 )
-from cdl.core.model.base import BaseProcParam, ResultProperties, ResultShape
-from cdl.core.model.image import ImageObj, ROI2DParam, RoiDataGeometries, RoiDataItem
-from cdl.core.model.signal import SignalObj
+from cdl.config import _
+from cdl.obj import (
+    BaseProcParam,
+    ImageObj,
+    ImageRoiDataItem,
+    ResultProperties,
+    ResultShape,
+    ROI2DParam,
+    RoiDataGeometries,
+    SignalObj,
+)
 
 VALID_DTYPES_STRLIST = ImageObj.get_valid_dtypenames()
 
@@ -62,7 +69,7 @@ class Wrap11Func:
     Example:
 
         >>> import numpy as np
-        >>> from cdl.core.computation.signal import Wrap11Func
+        >>> from cdl.computation.signal import Wrap11Func
         >>> import cdl.obj
         >>> def add_noise(data):
         ...     return data + np.random.random(data.shape)
@@ -1191,7 +1198,7 @@ def compute_magnitude_spectrum(
         Output image object
     """
     dst = dst_11(src, "magnitude_spectrum")
-    log_scale = True if p is not None and p.log else False
+    log_scale = p is not None and p.log
     dst.data = alg.magnitude_spectrum(src.data, log_scale=log_scale)
     dst.xunit = dst.yunit = dst.zunit = ""
     dst.xlabel = dst.ylabel = _("Frequency")
@@ -1224,7 +1231,7 @@ def compute_psd(src: ImageObj, p: SpectrumParam | None = None) -> ImageObj:
         Output image object
     """
     dst = dst_11(src, "psd")
-    log_scale = True if p is not None and p.log else False
+    log_scale = p is not None and p.log
     dst.data = alg.psd(src.data, log_scale=log_scale)
     dst.xunit = dst.yunit = dst.zunit = ""
     dst.xlabel = dst.ylabel = _("Frequency")
@@ -1351,7 +1358,7 @@ def calc_resultshape(
                 # Circle [x0, y0, r] or ellipse coordinates [x0, y0, a, b, theta]
                 colx, coly = 0, 1
             if obj.roi is not None:
-                x0, y0, _x1, _y1 = RoiDataItem(obj.roi[i_roi]).get_rect()
+                x0, y0, _x1, _y1 = ImageRoiDataItem(obj.roi[i_roi]).get_rect()
                 coords[:, colx] += x0
                 coords[:, coly] += y0
             coords[:, colx] = obj.dx * coords[:, colx] + obj.x0

cdl/core/computation/image/detection.py cdl/computation/image/detection.pycdl/core/computation/image/detection.py renamed to cdl/computation/image/detection.py

@@ -10,7 +10,7 @@
 
 # Note:
 # ----
-# All dataset classes must also be imported in the cdl.core.computation.param module.
+# All dataset classes must also be imported in the cdl.computation.param module.
 
 from __future__ import annotations
 
@@ -24,10 +24,9 @@
     get_2d_peaks_coords,
     get_contour_shapes,
 )
+from cdl.computation.image import calc_resultshape
 from cdl.config import _
-from cdl.core.computation.image import calc_resultshape
-from cdl.core.model.base import ResultShape, ShapeTypes
-from cdl.core.model.image import ImageObj
+from cdl.obj import ImageObj, ResultShape, ShapeTypes
 
 
 class GenericDetectionParam(gds.DataSet):

cdl/core/computation/image/edges.py cdl/computation/image/edges.pycdl/core/computation/image/edges.py renamed to cdl/computation/image/edges.py

@@ -10,17 +10,17 @@
 
 # Note:
 # ----
-# All dataset classes must also be imported in the cdl.core.computation.param module.
+# All dataset classes must also be imported in the cdl.computation.param module.
 
 from __future__ import annotations
 
 import guidata.dataset as gds
 import numpy as np
 from skimage import feature, filters
 
+from cdl.computation.image import Wrap11Func, dst_11
 from cdl.config import _
-from cdl.core.computation.image import Wrap11Func, dst_11
-from cdl.core.model.image import ImageObj
+from cdl.obj import ImageObj
 
 
 class CannyParam(gds.DataSet):

cdl/core/computation/image/exposure.py cdl/computation/image/exposure.pycdl/core/computation/image/exposure.py renamed to cdl/computation/image/exposure.py

@@ -10,16 +10,16 @@
 
 # Note:
 # ----
-# All dataset classes must also be imported in the cdl.core.computation.param module.
+# All dataset classes must also be imported in the cdl.computation.param module.
 
 from __future__ import annotations
 
 import guidata.dataset as gds
 from skimage import exposure
 
+from cdl.computation.image import VALID_DTYPES_STRLIST, dst_11
 from cdl.config import _
-from cdl.core.computation.image import VALID_DTYPES_STRLIST, dst_11
-from cdl.core.model.image import ImageObj
+from cdl.obj import ImageObj
 
 
 class AdjustGammaParam(gds.DataSet):

cdl/core/computation/image/morphology.py cdl/computation/image/morphology.pycdl/core/computation/image/morphology.py renamed to cdl/computation/image/morphology.py

@@ -10,16 +10,16 @@
 
 # Note:
 # ----
-# All dataset classes must also be imported in the cdl.core.computation.param module.
+# All dataset classes must also be imported in the cdl.computation.param module.
 
 from __future__ import annotations
 
 import guidata.dataset as gds
 from skimage import morphology
 
+from cdl.computation.image import dst_11
 from cdl.config import _
-from cdl.core.computation.image import dst_11
-from cdl.core.model.image import ImageObj
+from cdl.obj import ImageObj
 
 
 class MorphologyParam(gds.DataSet):

cdl/core/computation/image/restoration.py cdl/computation/image/restoration.pycdl/core/computation/image/restoration.py renamed to cdl/computation/image/restoration.py

@@ -10,7 +10,7 @@
 
 # Note:
 # ----
-# All dataset classes must also be imported in the cdl.core.computation.param module.
+# All dataset classes must also be imported in the cdl.computation.param module.
 
 from __future__ import annotations
 
@@ -19,10 +19,10 @@
 from skimage import morphology
 from skimage.restoration import denoise_bilateral, denoise_tv_chambolle, denoise_wavelet
 
+from cdl.computation.image import dst_11
+from cdl.computation.image.morphology import MorphologyParam
 from cdl.config import _
-from cdl.core.computation.image import dst_11
-from cdl.core.computation.image.morphology import MorphologyParam
-from cdl.core.model.image import ImageObj
+from cdl.obj import ImageObj
 
 
 class DenoiseTVParam(gds.DataSet):