fixing docs, README, DLK docstrings

README.md

@@ -85,22 +85,6 @@ video.set_points(points=p)
 ```
 Or use point selection UI to set individual points or grid inside selected area. For more information about UI see [documentation](https://pyidi.readthedocs.io/en/quick_start/napari.html). Launch viewer with:
 
-```
-video.gui()
-```
-
-The method of identification has to be specified:
-```
-video.set_method(method='sof', **method_kwargs)
-```
-After points are set, displacements can be calculated (using method, set in `set_method`):
-```
-displacements = video.get_displacements()
-```
-Multiprocessing can also be used by passing the `processes` argument:
-```
-displacements = video.get_displacements(processes=4)
-```
 
 # DEVELOPER GUIDELINES:
 * Add _name_of_method.py with class that inherits after `IDIMethods`

docs/source/code/modules.rst

@@ -25,6 +25,11 @@ The Lucas-Kanade algorithm for translations
 .. automodule:: pyidi.methods._lucas_kanade
     :members:
 
+Directional Lucas-Kanade
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. automodule:: pyidi.methods._directional_lucas_kanade
+    :members:
+
 Postprocessing
 --------------
 

docs/source/quick_start/basic_usage.rst

@@ -18,11 +18,36 @@ The basic usage of the package is presented.
 
 Loading the video
 -----------------
-First create the :py:class:`pyIDI <pyidi.pyidi.pyIDI>` object:
+First create the :py:class:`VideoReader <pyidi.video_reader.VideoReader>` object:
 
 .. code:: python
 
-    video = pyidi.pyIDI('filename.cih')
+    from pyidi import VideoReader
+
+    video = VideoReader('filename.cih')
+
+Setting the method
+------------------
+The video object must be passed to the :py:class:`IDIMethod <pyidi.methods.idi_method.IDIMethod>` class.
+Available methods are: 
+
+* :py:class:`SimplifiedOpticalFlow <pyidi.methods._simplified_optical_flow.SimplifiedOpticalFlow>`
+
+* :py:class:`LucasKanade <pyidi.methods._lucas_kanade.LucasKanade>`
+
+* :py:class:`DirectionalLucasKanade <pyidi.methods._directional_lucas_kanade.DirectionalLucasKanade>`
+
+To use the Simplified Optical Flow method, the object must be instantiated:
+
+.. code:: python
+
+    from pyidi import SimplifiedOpticalFlow
+    
+    sof = SimplifiedOpticalFlow(video)
+
+After the method object is instantiated, the points can be set and the arguments can be configured.
+
+For more details on the available methods, see the currently implemented :ref:`implemented_disp_id_methods`.
 
 Setting the points
 ------------------
@@ -38,38 +63,30 @@ Points must be of shape ``n_points x 2``:
 
 where the first column indicates indices along **axis 0**, and the second column indices along **axis 1**.
 
-The points must be passed to ``pyIDI`` object:
+The points must be passed to ``method`` object:
 
 .. code:: python
 
-    video.set_points(points=points)
+    sof.set_points(points=points)
 
 If the points are not known, a :ref:`point-selection` or newer :ref:`napari` can be used to select the points.
 
-Setting the method
-------------------
-The method for displacement identification must be selected:
-
-.. code:: python
-
-    video.set_method(method='sof') # Simplified optical flow method
-
-After the method is selected, the arguments can be configured. Note that the docstring is now
-showing the required arguments for the selected method.
+Configuring the method
+----------------------
+The method can be configured using:
 
 .. code:: python
+    
+    sof.configure(...)
 
-    video.method.configure(*args, **kwargs)
-
-For more details on the available methods, see the currently implemented :ref:`implemented_disp_id_methods`.
 
 Get displacement
 ----------------
 Finally, displacements can be identified:
 
 .. code:: python
 
-    displacements = video.get_displacements()
+    displacements = sof.get_displacements()
 
 Saved analysis
 --------------

docs/source/quick_start/disp_id_methods.rst

@@ -11,4 +11,9 @@ Simplified Optical Flow (SOF)
 Lucas-Kanade (LK)
 -----------------
 
-    [2] Lucas, B. D., & Kanade, T. (1981). An Iterative Image Registration Technique with an Application to Stereo Vision. In Proceedings of the 7th International Joint Conference on Artificial Intelligence - Volume 2 (pp. 674–679). San Francisco, CA, USA: Morgan Kaufmann Publishers Inc. Retrieved from http://dl.acm.org/citation.cfm?id=1623264.1623280
+    [2] Lucas, B. D., & Kanade, T. (1981). An Iterative Image Registration Technique with an Application to Stereo Vision. In Proceedings of the 7th International Joint Conference on Artificial Intelligence - Volume 2 (pp. 674–679). San Francisco, CA, USA: Morgan Kaufmann Publishers Inc. Retrieved from http://dl.acm.org/citation.cfm?id=1623264.1623280
+
+Directional DIC
+------------------------
+
+    [3] Masmeijer T., Habtour E., Zaletelj K. & Slavič J. (2025). Directional DIC method with automatic feature selection. Mechanical Systems and Signal Processing, 224. https://doi.org/10.1016/j.ymssp.2024.112080

pyidi/methods/_directional_lucas_kanade.py

@@ -50,7 +50,7 @@ def configure(
         :param roi_size: (h, w) height and width of the region of interest.
             ROI dimensions should be odd numbers. Defaults to (9, 9)
         :type roi_size: tuple, list, optional
-        :param dij: Assumed vibration direction. Must be |d|=1. Convention is 'negative down, positive right'.
+        :param dij: Assumed vibration direction. Must be \\|d\\|=1. Convention is 'negative down, positive right'.
         :type dij: tuple, list, optional
         :param pad: size of padding around the region of interest in px, defaults to 2
         :type pad: int, optional
@@ -69,7 +69,7 @@ def configure(
         :param processes: number of processes to run
         :type processes: int, optional, defaults to 1.
         :param resume_analysis: if True, the last analysis results are loaded and computation continues from last computed time point.
-        :type resum_analysis: bool, optional
+        :type resume_analysis: bool, optional
         :param reference_image: The reference image for computation. Can be index of a frame, tuple (slice) or numpy.ndarray that
             is taken as a reference.
         :type reference_image: int or tuple or ndarray
@@ -306,22 +306,21 @@ def optimize_translations(self, G, F_spline, maxiter, tol, dij, d_subpixel_init=
 
 
     def _padded_slice(self, point, roi_size, image_shape, pad=None):
-        '''
+        """
         Returns a slice that crops an image around a given `point` center, 
         `roi_size` and `pad` size. If the resulting slice would be out of
         bounds of the image to be sliced (given by `image_shape`), the
         slice is snifted to be on the image edge and a warning is issued.
         :param point: The center point coordiante of the desired ROI.
         :type point: array_like of size 2, (y, x)
         :param roi_size: Size of desired cropped image (y, x).
-        type roi_size: array_like of size 2, (h, w)
+        :type roi_size: array_like of size 2, (h, w)
         :param image_shape: Shape of the image to be sliced, (h, w).
-        type image_shape: array_like of size 2, (h, w)
-        :param pad: Pad border size in pixels. If None, the video.pad
-            attribute is read.
+        :type image_shape: array_like of size 2, (h, w)
+        :param pad: Pad border size in pixels. If None, the video.pad attribute is read.
         :type pad: int, optional, defaults to None
         :return crop_slice: tuple (yslice, xslice) to use for image slicing.
-        '''
+        """
 
         if pad is None:
             pad = self.pad

pyidi/pyidi.py

@@ -8,7 +8,7 @@
 import warnings
 warnings.simplefilter("default")
 
-from .methods import IDIMethod, SimplifiedOpticalFlow, LucasKanade, LucasKanadeSc, LucasKanadeSc2, GradientBasedOpticalFlow, DirectionalLucasKanade
+from .methods import IDIMethod, SimplifiedOpticalFlow, LucasKanade, DirectionalLucasKanade #, LucasKanadeSc, LucasKanadeSc2, GradientBasedOpticalFlow
 from .video_reader import VideoReader
 from . import tools
 from . import selection