New api

.gitignore

@@ -125,4 +125,5 @@ server_user_id.txt
 
 /temp
 
-data_synthetic_pyidi_analysis/
+data_synthetic_pyidi_analysis/
+temp_file/

README.md

@@ -6,14 +6,83 @@ Image-based Displacement Identification (IDI) implementation in python.
 
 See the [documentation](https://pyidi.readthedocs.io/en/latest/index.html) for `pyIDI`.
 
-### Use Napari UI for quick displacement identification:
+## Now version 1.0!
+
+In version 1.0, **we overhauled the package API**. With growing usage in IDEs other than
+jupyter notebooks, we have made the package more user-friendly. The new API allows the
+autocompletion and documentation of the package to be more accessible in IDEs like
+VSCode, Cursor, PyCharm, etc.
+
+To install the new version, use the following command:
+
+```bash
+pip install pyidi
+```
+or to upgrade (if already installed):
+```bash
+pip install -U pyidi
+```
+
+### Whats different?
+
+For the user, the main difference is that instead of calling the `pyIDI` class where the
+method is set, first, the `VideoReader` class is called. Then, this instance is passed
+to the specific method class. Here is an example:
+
+```python
+from pyidi import VideoReader, SimplifiedOpticalFlow
+
+# Read the video
+video = VideoReader('video.cih')
+
+# Pass the video to the selected method class
+sof = SimplifiedOpticalFlow(video)
+
+sof.set_points(points=[[0, 1], [1, 1], [2, 1]])
+sof.configure(...)
+displacements = sof.get_displacements()
+```
+
+The methods themselves have not changed, only the way they are called. Unfortunately, this
+breaks the backward compatibility with the previous version. We apologize for any
+inconvenience this may cause. To keep using the old version, please install the package
+with the following command:
+
+```bash
+pip install pyidi==0.30.2
+```
+
+or use the legacy `pyIDI` class:
+
+```python
+from pyidi import pyIDI
+```
+
+Note that the legacy `pyIDI` class does not necessarily offer the full functionality of the new version. 
+The legacy `pyIDI` class is only kept for compatibility with the old version and will not be updated.
+
+
+# Use Napari UI for quick displacement identification:
 <img src="docs/source/quick_start/gifs/napari_full_sof.gif" width="800" />
 
 
 # BASIC USAGE:
-Create an instance:
+Run GUI by instantiating GUI class (input is VideoReader object):
+```python
+from pyidi import VideoReader, GUI
+
+# Read the video
+video = VideoReader('data/data_synthetic.cih')
+
+# Run GUI
+gui = GUI(video)
 ```
-video = pyidi.pyIDI(input_file='video.cih')
+
+Method class (e.g. `SimplifiedOpticalFlow`) is instantiated during the use of GUI. It is accessible in `gui.method`. To get displacements:
+
+```python
+method = gui.method
+displacements = method.displacements
 ```
 
 The `pyIDI` method works with various formats: `.cih`, `.cihx`, `.png`, `.avi` etc. Additionally, it can also work with `numpy.ndarray` as input.
@@ -26,22 +95,6 @@ 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`

Showcas_LK.ipynb

@@ -30,7 +30,7 @@
    "outputs": [],
    "source": [
     "filename = 'data/data_synthetic.cih'\n",
-    "video = pyidi.pyIDI(filename)"
+    "video = pyidi.VideoReader(filename)"
    ]
   },
   {
@@ -71,7 +71,7 @@
     }
    ],
    "source": [
-    "video.reader.info"
+    "video.info"
    ]
   },
   {
@@ -87,14 +87,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Points = pyidi.selection.ROISelect(video, roi_size=(21, 21), noverlap=0)"
+    "Points = pyidi.selection.SubsetSelection(video, roi_size=(11, 11), noverlap=0)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Assigning the points"
+    "Create the `LucasKanade` object"
    ]
   },
   {
@@ -103,14 +103,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# video.set_points(Points.points)"
+    "idi = pyidi.LucasKanade(video)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Assign the `Lucas Kanade` method"
+    "Assigning the points"
    ]
   },
   {
@@ -119,17 +119,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "video.set_method('lk')\n",
-    "\n",
-    "reference_image = video.method._set_reference_image(video, video.method.reference_image)\n",
-    "Gi, Gj = np.gradient(reference_image)\n",
-    "G = np.sqrt(Gi**2 + Gj**2)\n",
-    "highest_points = np.argpartition(G.flatten(), -10)[-10:]\n",
-    "arguments = np.unravel_index(highest_points, G.shape)\n",
-    "points1d = np.array(arguments).T\n",
-    "video.set_points(points1d)\n",
-    "\n",
-    "video.method.configure()"
+    "idi.set_points(Points) # The `Points` object can be passed directly to the `set_points` method"
    ]
   },
   {
@@ -147,7 +137,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "51a62fe6402f43bf923beb7de0c519e0",
+       "model_id": "843cc35f2b764d969e5d59eca39a6b8c",
        "version_major": 2,
        "version_minor": 0
       },
@@ -164,7 +154,7 @@
      "text": [
       "--- Starting new analysis ---\n",
       " \n",
-      "Computation start: 2024-11-26 13:39:44.382596\n"
+      "Computation start: 2024-12-03 07:41:27.317520\n"
      ]
     },
     {
@@ -181,14 +171,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Computation duration: 00:00:2.56\n",
-      "data\\data_synthetic_pyidi_analysis\\analysis_006\\ analysis_006\n"
+      "Computation duration: 00:00:2.26\n",
+      "data\\data_synthetic_pyidi_analysis\\analysis_009\\ analysis_009\n"
      ]
     }
    ],
    "source": [
-    "if __name__ == '__main__':\n",
-    "    displacementes = video.get_displacements(processes=2)"
+    "displacementes = idi.get_displacements(processes=2)"
    ]
   },
   {
@@ -198,86 +187,25 @@
     "An existing analysis can also be loaded without computation and setting the arguments."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "d:\\git_repos\\pyidi\\pyidi\\load_analysis.py:30: ResourceWarning: unclosed file <_io.BufferedReader name='data/data_synthetic_pyidi_analysis/analysis_001\\\\points.pkl'>\n",
-      "  points = pickle.load(open(os.path.join(analysis_path, 'points.pkl'), 'rb'))\n",
-      "ResourceWarning: Enable tracemalloc to get the object allocation traceback\n",
-      "d:\\git_repos\\pyidi\\pyidi\\load_analysis.py:32: ResourceWarning: unclosed file <_io.BufferedReader name='data/data_synthetic_pyidi_analysis/analysis_001\\\\results.pkl'>\n",
-      "  results = pickle.load(open(os.path.join(analysis_path, 'results.pkl'), 'rb'))\n",
-      "ResourceWarning: Enable tracemalloc to get the object allocation traceback\n"
-     ]
-    }
-   ],
-   "source": [
-    "filename = 'data/data_synthetic_pyidi_analysis/analysis_001'\n",
-    "video_loaded, info_dict = pyidi.load_analysis(filename,)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "(10, 101, 2)"
-      ]
-     },
-     "execution_count": 9,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "video_loaded.displacements.shape"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 10,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "(10, 2)"
-      ]
-     },
-     "execution_count": 10,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "points1d.shape"
+    "filename = 'data/data_synthetic_pyidi_analysis/analysis_010'\n",
+    "video_loaded, idi_loaded, info_dict = pyidi.load_analysis(filename)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 11,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "d:\\git_repos\\pyidi\\pyidi\\pyidi.py:266: DeprecationWarning: `self.mraw` is deprecated and will be removed in the next version. Please use `self.reader.mraw` instead.\n",
-      "  warnings.warn('`self.mraw` is deprecated and will be removed in the next version. Please use `self.reader.mraw` instead.', DeprecationWarning)\n"
-     ]
-    },
     {
      "data": {
       "text/plain": [
-       "(101, 128, 256)"
+       "(5, 101, 2)"
       ]
      },
      "execution_count": 11,
@@ -286,7 +214,7 @@
     }
    ],
    "source": [
-    "video_loaded.mraw.shape"
+    "idi_loaded.displacements.shape"
    ]
   },
   {