back2raw results to json and png

fix #51 and #20

docs/jupyter/backward_projection.ipynb

@@ -306,6 +306,29 @@
     "```"
    ]
   },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "\n",
+    "<div class=\"alert alert-info\">\n",
+    "\n",
+    "Note\n",
+    "\n",
+    "You can save the results (json and cropped png) to given folder by:\n",
+    "\n",
+    "```python\n",
+    "img_dict_sort = roi.back2raw(ms, ..., save_folder=\"folder_to_save\")\n",
+    "```\n",
+    "\n",
+    "And will get the following results in the folder:\n",
+    "\n",
+    "<center><img src=\"../_static/images/python_api/back2raw_save.png\" alt=\"lotus plot\" width=\"50%\"/></center>\n",
+    "\n",
+    "</div>\n"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -548,6 +571,28 @@
     ")"
    ]
   },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-info\">\n",
+    "\n",
+    "Note\n",
+    "\n",
+    "You can save the results (json and cropped png) to given folder by:\n",
+    "\n",
+    "```python\n",
+    "img_dict_sort = ms.sort_img_by_distance(..., save_folder=\"folder_to_save\")\n",
+    "```\n",
+    "\n",
+    "And will get the following results in the folder:\n",
+    "\n",
+    "<center><img src=\"../_static/images/python_api/back2raw_sort.png\" alt=\"lotus plot\" width=\"50%\"/></center>\n",
+    "\n",
+    "</div>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 14,
@@ -703,7 +748,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.8.13 (default, Mar 28 2022, 06:16:26) \n[Clang 12.0.0 ]"
   },
   "vscode": {
    "interpreter": {

easyidp/data.py

@@ -472,6 +472,7 @@ def __init__(self, test_out="./tests/out"):
 
         self.cv = self.CVDataset(self.data_dir, test_out)
         self.vis = self.VisualDataset(self.data_dir, test_out)
+        self.b2r = self.Back2rawDataset(self.data_dir, test_out)
 
 
     class MetashapeDataset():
@@ -646,3 +647,17 @@ def __init__(self, data_dir, test_out):
 
         def __truediv__(self, other):
             return self.data_dir / "visual_test" / other
+
+
+
+    class Back2rawDataset():
+
+        def __init__(self, data_dir, test_out):
+            self.data_dir = data_dir
+
+            if isinstance(test_out, str):
+                test_out = Path(test_out)
+            self.out = test_out / "back2raw_test"
+
+        def __truediv__(self, other):
+            return self.data_dir / "back2raw_test" / other

easyidp/metashape.py

@@ -442,7 +442,7 @@ def _back2raw_one2one(self, points_np, photo_id, distortion_correct=True):
         else:
             return out
 
-    def back2raw_crs(self, points_xyz, save_folder=None, ignore=None, log=False):
+    def back2raw_crs(self, points_xyz, ignore=None, log=False):
         """Projs one GIS coordintates ROI (polygon) to all images
 
         Parameters
@@ -457,11 +457,6 @@ def back2raw_crs(self, points_xyz, save_folder=None, ignore=None, log=False):
             - ``x``: only y (vertical) in image area, x can outside image;
             - ``y``: only x (horizontal) in image area, y can outside image.
 
-        save_folder : str | default ""
-            The folder to contain the output results (preview images and json coords)
-
-            .. caution:: This feature has not been implemented
-
         log : bool, optional
             whether print log for debugging, by default False
 
@@ -543,7 +538,7 @@ def back2raw(self, roi, save_folder=None, **kwargs):
         roi : easyidp.ROI | dict
             the <ROI> object created by easyidp.ROI() or dictionary
         save_folder : str, optional
-            the folder to save projected preview images and json files, by default ""
+            the folder to save json files and parts of ROI on raw images, by default None
         ignore : str | None, optional
             Whether tolerate small parts outside image, check 
             :func:`easyidp.reconstruct.Sensor.in_img_boundary` for more details.
@@ -619,11 +614,15 @@ def back2raw(self, roi, save_folder=None, **kwargs):
             if points_xyz.shape[1] != 3:
                 raise ValueError(f"The back2raw function requires 3D roi with shape=(n, 3), but [{k}] is {points_xyz.shape}")
 
-            one_roi_dict= self.back2raw_crs(points_xyz, save_folder=save_path, **kwargs)
+            one_roi_dict= self.back2raw_crs(points_xyz, **kwargs)
 
             out_dict[k] = one_roi_dict
 
         self.crs = before_crs
+
+        if save_folder is not None:
+            idp.reconstruct.save_back2raw_json_and_png(self, out_dict, save_folder)
+
         return out_dict
 
     def get_photo_position(self, to_crs=None, refresh=False):
@@ -714,7 +713,7 @@ def get_photo_position(self, to_crs=None, refresh=False):
             return out
 
 
-    def sort_img_by_distance(self, img_dict_all, roi, distance_thresh=None, num=None):
+    def sort_img_by_distance(self, img_dict_all, roi, distance_thresh=None, num=None, save_folder=None):
         """Advanced wrapper of sorting back2raw img_dict results by distance from photo to roi
 
         Parameters
@@ -728,6 +727,8 @@ def sort_img_by_distance(self, img_dict_all, roi, distance_thresh=None, num=None
             Keep the closest {x} images
         distance_thresh : None or float
             Keep the images closer than this distance to ROI.
+        save_folder : str, optional
+            the folder to save json files and parts of ROI on raw images, by default None
 
         Returns
         -------
@@ -851,7 +852,7 @@ def sort_img_by_distance(self, img_dict_all, roi, distance_thresh=None, num=None
         if not self.enabled:
             raise TypeError("Unable to process disabled chunk (.enabled=False)")
 
-        return idp.reconstruct.sort_img_by_distance(self, img_dict_all, roi, distance_thresh, num)
+        return idp.reconstruct.sort_img_by_distance(self, img_dict_all, roi, distance_thresh, num, save_folder)
 
     def show_roi_on_img(self, img_dict, roi_name, img_name=None, **kwargs):
         """Visualize the specific backward projection results for given roi on the given image.

easyidp/pix4d.py

@@ -519,7 +519,7 @@ def _pmatrix_calc(self, points, photo, distort_correct=True):
         return coords_b
 
 
-    def back2raw_crs(self, points_xyz, distort_correct=True, ignore=None, save_folder=None, log=False):
+    def back2raw_crs(self, points_xyz, distort_correct=True, ignore=None, log=False):
         """Projects one GIS coordintates ROI (polygon) to all images
 
         Parameters
@@ -538,11 +538,6 @@ def back2raw_crs(self, points_xyz, distort_correct=True, ignore=None, save_folde
             - ``x``: only y (vertical) in image area, x can outside image;
             - ``y``: only x (horizontal) in image area, y can outside image.
 
-        save_folder : str | default ""
-            The folder to contain the output results (preview images and json coords)
-
-            .. caution:: This feature has not been implemented
-
         log : bool, optional
             whether print log for debugging, by default False
 
@@ -606,13 +601,6 @@ def back2raw_crs(self, points_xyz, distort_correct=True, ignore=None, save_folde
             if coords is not None:
                 out_dict[photo.label] = coords
 
-        if isinstance(save_folder, str) and os.path.isdir(save_folder):
-            # if not os.path.exists(save_folder):
-            #     os.makedirs(save_folder)
-            # save to json file
-            # save to one image file ()
-            raise NotImplementedError("This feature has not been implemented")
-
         return out_dict
 
 
@@ -698,10 +686,13 @@ def back2raw(self, roi, save_folder=None, **kwargs):
                     f"The back2raw function requires 3D roi with shape=(n, 3)"
                     f", but [{k}] is {points_xyz.shape}")
 
-            one_roi_dict= self.back2raw_crs(points_xyz, save_folder=save_path, **kwargs)
+            one_roi_dict= self.back2raw_crs(points_xyz, **kwargs)
 
             out_dict[k] = one_roi_dict
 
+        if save_folder is not None:
+            idp.reconstruct.save_back2raw_json_and_png(self, out_dict, save_folder)
+
         return out_dict
 
     def get_photo_position(self, to_crs=None, refresh=False):
@@ -731,9 +722,7 @@ def get_photo_position(self, to_crs=None, refresh=False):
             >>> import easyidp as idp
 
             >>> lotus = idp.data.Lotus()
-            >>> p4d = idp.Pix4D(project_path=lotus.pix4d.project, 
-            >>>                 raw_img_folder=lotus.photo,
-            >>>                 param_folder=lotus.pix4d.param)
+            >>> p4d = idp.Pix4D(lotus.pix4d.project,lotus.photo, lotus.pix4d.param)
 
         Then use this function to get the photo position in 3D world:
 
@@ -774,7 +763,7 @@ def get_photo_position(self, to_crs=None, refresh=False):
 
             return out
 
-    def sort_img_by_distance(self, img_dict_all, roi, distance_thresh=None, num=None):
+    def sort_img_by_distance(self, img_dict_all, roi, distance_thresh=None, num=None, save_folder=None):
         """Advanced wrapper of sorting back2raw img_dict results by distance from photo to roi
 
         Parameters
@@ -788,6 +777,8 @@ def sort_img_by_distance(self, img_dict_all, roi, distance_thresh=None, num=None
             Keep the closest {x} images
         distance_thresh : None or float
             Keep the images closer than this distance to ROI.
+        save_folder : str, optional
+            the folder to save json files and parts of ROI on raw images, by default None
 
         Returns
         -------
@@ -913,7 +904,7 @@ def sort_img_by_distance(self, img_dict_all, roi, distance_thresh=None, num=None
         easyidp.reconstruct.sort_img_by_distance
 
         """
-        return idp.reconstruct.sort_img_by_distance(self, img_dict_all, roi, distance_thresh, num)
+        return idp.reconstruct.sort_img_by_distance(self, img_dict_all, roi, distance_thresh, num, save_folder)
 
     def show_roi_on_img(self, img_dict, roi_name, img_name=None, **kwargs):
         """Visualize the specific backward projection results for given roi on the given image.

easyidp/reconstruct.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 from tqdm import tqdm
 import warnings
+from skimage.io import imread, imsave
 
 import easyidp as idp
 
@@ -649,7 +650,7 @@ def _sort_img_by_distance_one_roi(recons, img_dict, plot_geo, cam_pos, distance_
     return img_dict_sort
 
 
-def sort_img_by_distance(recons, img_dict_all, roi, distance_thresh=None, num=None):
+def sort_img_by_distance(recons, img_dict_all, roi, distance_thresh=None, num=None, save_folder=None):
     """Advanced wrapper of sorting back2raw img_dict results by distance from photo to roi
 
     Parameters
@@ -665,6 +666,8 @@ def sort_img_by_distance(recons, img_dict_all, roi, distance_thresh=None, num=No
         Keep the closest {x} images
     distance_thresh : None or float
         Keep the images closer than this distance to ROI.
+    save_folder : str, optional
+        the folder to save json files and parts of ROI on raw images, by default None
 
     Returns
     -------
@@ -682,4 +685,83 @@ def sort_img_by_distance(recons, img_dict_all, roi, distance_thresh=None, num=No
         )
         img_dict_sort_all[roi_name] = sort_dict
 
-    return img_dict_sort_all
+    if save_folder is not None:
+        save_back2raw_json_and_png(recons, img_dict_sort_all, save_folder)
+
+    return img_dict_sort_all
+
+
+def save_back2raw_json_and_png(recons, results_dict, save_folder):
+    """Save the backward reversed results 
+
+    Parameters
+    ----------
+    results_dict : dict
+        the outputs of :func:`back2raw() <easyidp.roi.back2raw()>` function results
+    save_path : str
+        the folder to save output files
+
+    Example
+    -------
+
+    Data prepare
+
+    .. code-block:: python
+
+        >>> import easyidp as idp
+        >>> lotus = idp.data.Lotus()
+        >>> p4d = idp.Pix4D(lotus.pix4d.project, lotus.photo, lotus.pix4d.param)
+
+        >>> roi = idp.ROI(lotus.shp, name_field=0)
+        >>> roi = roi[0:3]
+        >>> roi.get_z_from_dsm(lotus.pix4d.dsm)
+
+        >>> out_p4d = roi.back2raw(p4d)
+
+    Use this function:
+
+    .. code-block:: python
+
+        >>> idp.reconstruct.save_back2raw_json_and_png(p4d, out_p4d, "out_path")
+
+    """
+    # prepare the root folder
+    if isinstance(save_folder, (str, Path)):
+        save_folder = str(save_folder)
+        if not os.path.exists(save_folder):
+            os.makedirs(save_folder)
+    else:
+        raise TypeError(f"Only the string path is acceptable, not [{save_folder} {type(save_folder)}]")
+
+    # reverse the current order results_dict[roi][image_name] to results[image_name][roi]
+    # this will save the IO cost when loading images.
+    print("Optimising data structures of produced results, this may take some time...")
+    rev_dict = {}
+    for roi_name, roi_dict in results_dict.items():
+        # create the save path of each roi
+        roi_folder = os.path.join(save_folder, roi_name)
+        if not os.path.exists(roi_folder):
+            os.mkdir(roi_folder)
+
+        for img_name, img_pos in roi_dict.items():
+            if img_name not in rev_dict.keys():
+                rev_dict[img_name] = {}
+
+            rev_dict[img_name][roi_name] = img_pos
+
+    # save the full results as json directly
+    idp.jsonfile.save_json(results_dict, os.path.join(save_folder, "roi_image_order.json"))
+    idp.jsonfile.save_json(rev_dict, os.path.join(save_folder, "image_roi_order.json"))
+
+    # then doing the for loop for each image.
+    for img_name, img_rois in tqdm(rev_dict.items(), desc=f"Processing image [{img_name}]"):
+
+        img_array = imread(recons.photos[img_name].path)
+
+        for roi_name, img_pos in tqdm(img_rois.items(), leave=False):
+
+            png_save_path = os.path.join(save_folder, roi_name, f"{roi_name}_{img_name}.png")
+
+            cropped_png, _ = idp.cvtools.imarray_crop(img_array, img_pos)
+
+            imsave(png_save_path, cropped_png)

easyidp/roi.py

@@ -873,7 +873,7 @@ def crop(self, target, save_folder=None):
 
         return out
 
-    def back2raw(self, recons, save_folder=None, **kwargs):
+    def back2raw(self, recons, **kwargs):
         """Projects several GIS coordintates ROIs (polygons) to all images
 
         Parameters
@@ -948,9 +948,7 @@ def back2raw(self, recons, save_folder=None, **kwargs):
             >>> import easyidp as idp
             >>> lotus = idp.data.Lotus()
 
-            >>> p4d = idp.Pix4D(project_path=lotus.pix4d.project, 
-            ...                 raw_img_folder=lotus.photo,
-            ...                 param_folder=lotus.pix4d.param)
+            >>> p4d = idp.Pix4D(lotus.pix4d.project, lotus.photo, lotus.pix4d.param)
 
             >>> ms = idp.Metashape(project_path=lotus.metashape.project, chunk_id=0)
 
@@ -1090,6 +1088,7 @@ def load_detections(path):
     """
 
     # boxes = pd.read_csv(path)
+    boxes = None
     if not all([x in ["image_path","xmin","ymin","xmax","ymax","image_path","label"] for x in boxes.columns]):
         raise IOError("{} is expected to be a .csv with columns, xmin, ymin, xmax, ymax, image_path, label for each detection")