Merge pull request #31 from domengorjup/master

Fix backwards compatibility issues with pyIDI.info, pyIDI.close_video() and analyzing ndarray videos.
ladisk · May 16, 2024 · 60a05a3 · 60a05a3
2 parents 4fe81c4 + 2eab861
commit 60a05a3
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Showing 5 changed files with 218 additions and 201 deletions.
diff --git a/.gitignore b/.gitignore
@@ -121,4 +121,6 @@ dmypy.json
 /data/*.pkl
 
 #other
-server_user_id.txt
+server_user_id.txt
+
+/temp
diff --git a/Showcas_LK.ipynb b/Showcas_LK.ipynb
@@ -2,9 +2,20 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "C:\\Users\\Domen\\AppData\\Local\\Programs\\Python\\Python312\\Lib\\copy.py:151: DeprecationWarning: Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.\n",
+      "  rv = reductor(4)\n",
+      "C:\\Users\\Domen\\AppData\\Local\\Programs\\Python\\Python312\\Lib\\copy.py:261: DeprecationWarning: Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.\n",
+      "  y.__setstate__(state)\n"
+     ]
+    }
+   ],
    "source": [
     "import os\n",
     "import sys\n",
@@ -25,7 +36,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,9 +53,34 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'Date': '2016/08/31',\n",
+       " 'Camera Type': 1,\n",
+       " 'Record Rate(fps)': 1,\n",
+       " 'Shutter Speed(s)': 1.0,\n",
+       " 'Total Frame': 101,\n",
+       " 'Original Total Frame': 101,\n",
+       " 'Start Frame': 0,\n",
+       " 'Image Width': 256,\n",
+       " 'Image Height': 128,\n",
+       " 'Color Type': 'Mono',\n",
+       " 'Color Bit': 16,\n",
+       " 'File Format': 'MRaw',\n",
+       " 'EffectiveBit Depth': 12,\n",
+       " 'EffectiveBit Side': 'Lower',\n",
+       " 'Comment Text': 'Generated sequence.<br>Modify measurement info in<br>created .cih file if necessary.'}"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "video.reader.info"
    ]
@@ -58,7 +94,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +110,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -90,7 +126,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -106,9 +142,41 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "--- Starting new analysis ---\n",
+      " \n",
+      "Computation start: 2024-05-16 08:37:22.807458\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "13430c29596e4052b53b0ac8b85e5442",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "VBox()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Computation duration: 00:00:6.88\n",
+      "data\\data_synthetic_pyidi_analysis\\analysis_004\\ analysis_004\n"
+     ]
+    }
+   ],
    "source": [
     "displacementes = video.get_displacements(processes=2)"
    ]
@@ -122,26 +190,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
     "filename = 'data/data_synthetic_pyidi_analysis/analysis_001'\n",
     "video_loaded, info_dict = pyidi.load_analysis(filename, )"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "hide_input": false,
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -155,7 +216,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.12.2"
   },
   "toc": {
    "base_numbering": 1,
@@ -172,5 +233,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/Showcase.ipynb b/Showcase.ipynb
diff --git a/pyidi/pyidi.py b/pyidi/pyidi.py
@@ -187,13 +187,11 @@ def get_displacements(self, autosave=True, **kwargs):
             raise ValueError('IDI method has not yet been set. Please call `set_method()` first.')
 
 
-    # def close_video(self):
-    #     """
-    #     Close the .mraw video memmap.
-    #     """
-    #     if hasattr(self, 'mraw'):
-    #         self.mraw._mmap.close()
-    #         del self.mraw
+    def close_video(self):
+        """
+        Close the .mraw video memmap.
+        """
+        self.reader.close()
 
 
     def create_analysis_directory(self):
@@ -230,7 +228,7 @@ def save(self, root=''):
                 'N': self.reader.N
             },
             'createdate': datetime.datetime.now().strftime("%Y %m %d    %H:%M:%S"),
-            'cih_file': self.cih_file,
+            'cih_file': self.cih_file if type(self.cih_file) == str else 'ndarray',
             'settings': self.method.create_settings_dict(),
             'method': self.method_name
         }
@@ -269,6 +267,11 @@ def gui(self):
     def mraw(self):
         warnings.warn('`self.mraw` is deprecated and will be removed in the next version. Please use `self.reader.mraw` instead.', DeprecationWarning)
         return self.reader.mraw
+
+    @property
+    def info(self):
+        #warnings.warn('`self.info` is deprecated and will be removed in the next version. Please use `self.reader.info` instead.', DeprecationWarning)
+        return self.reader.info
 
 #     def gui(self):
 #         """Napari interface.

diff --git a/pyidi/video_reader.py b/pyidi/video_reader.py
@@ -60,6 +60,7 @@ def __init__(self, input_file, root=None):
             self.N = info['Total Frame']
             self.image_width = info['Image Width']
             self.image_height = info['Image Height']
+            self.info = info
 
         elif self.file_format in SUPPORTED_IMAGE_FORMATS:
             image_prop = iio.improps(input_file)
@@ -189,6 +190,15 @@ def _get_frame_from_video_file(self, frame_number, use_channel='Y'):
             raise ValueError('Unsupported channel! Only R, G, B and Y are supported.')
 
         return image
+
+    def close(self):
+        """
+        Close the video and clear the resources.
+        In case of a MRAW video, closes the memory map for "mraw" file format.
+        """
+        if hasattr(self, 'mraw') and self.file_format in PHORTRON_HEADER_FILE:
+            self.mraw._mmap.close()
+            del self.mraw
 
 def _rgb2luma(rgb_image):
     """Converts "RGB" image to "YUV" and returns only "Y" (luma) component.