docs: clarify volumetric array axis order is WHD (X,Y,Z), not HWD

monai/apps/vista3d/inferer.py

@@ -45,14 +45,17 @@ def point_based_window_inferer(
     patch inference and average output stitching, and finally returns the segmented mask.
 
     Args:
-        inputs: [1CHWD], input image to be processed.
+        inputs: [1CWHD], input image to be processed (spatial axes are in
+            Width, Height, Depth order; i.e., for [N, C, W, H, D], Width is
+            axis 2, Height is axis 3, Depth is axis 4, matching arrays
+            returned by MONAI's NIfTI/ITK readers).
         roi_size: the spatial window size for inferences.
             When its components have None or non-positives, the corresponding inputs dimension will be used.
             if the components of the `roi_size` are non-positive values, the transform will use the
             corresponding components of img size. For example, `roi_size=(32, -1)` will be adapted
             to `(32, 64)` if the second spatial dimension size of img is `64`.
         sw_batch_size: the batch size to run window slices.
-        predictor: the model. For vista3D, the output is [B, 1, H, W, D] which needs to be transposed to [1, B, H, W, D].
+        predictor: the model. For vista3D, the output is [B, 1, W, H, D] which needs to be transposed to [1, B, W, H, D].
             Add transpose=True in kwargs for vista3d.
         point_coords: [B, N, 3]. Point coordinates for B foreground objects, each has N points.
         point_labels: [B, N]. Point labels. 0/1 means negative/positive points for regular supported or zero-shot classes.
@@ -61,13 +64,13 @@ def point_based_window_inferer(
         prompt_class: [B]. The same as class_vector representing the point class and inform point head about
             supported class or zeroshot, not used for automatic segmentation. If None, point head is default
             to supported class segmentation.
-        prev_mask: [1, B, H, W, D]. The value is before sigmoid. An optional tensor of previously segmented masks.
+        prev_mask: [1, B, W, H, D]. The value is before sigmoid. An optional tensor of previously segmented masks.
         point_start: only use points starting from this number. All points before this number is used to generate
             prev_mask. This is used to avoid re-calculating the points in previous iterations if given prev_mask.
         center_only: for each point, only crop the patch centered at this point. If false, crop 3 patches for each point.
         margin: if center_only is false, this value is the distance between point to the patch boundary.
     Returns:
-        stitched_output: [1, B, H, W, D]. The value is before sigmoid.
+        stitched_output: [1, B, W, H, D]. The value is before sigmoid.
     Notice: The function only supports SINGLE OBJECT INFERENCE with B=1.
     """
     if not point_coords.shape[0] == 1:

monai/data/image_writer.py

@@ -226,8 +226,11 @@ def resample_if_needed(
         transformation computed from ``affine`` and ``target_affine``.
 
         This function assumes the NIfTI dimension notations. Spatially it
-        supports up to three dimensions, that is, H, HW, HWD for 1D, 2D, 3D
-        respectively. When saving multiple time steps or multiple channels,
+        supports up to three dimensions, that is, ``W``, ``WH``, ``WHD`` for
+        1D, 2D, 3D respectively (equivalently ``X``, ``XY``, ``XYZ``; axis 0
+        is columns/Width, axis 1 is rows/Height, axis 2 is Depth/slices,
+        matching the array order returned by NIfTI/ITK readers). When saving
+        multiple time steps or multiple channels,
         time and/or modality axes should be appended after the first three
         dimensions. For example, shape of 2D eight-class segmentation
         probabilities to be saved could be `(64, 64, 1, 8)`. Also, data in
@@ -303,8 +306,8 @@ def convert_to_channel_last(
                 ``None`` indicates no channel dimension, a new axis will be appended as the channel dimension.
                 a sequence of integers indicates multiple non-spatial dimensions.
             squeeze_end_dims: if ``True``, any trailing singleton dimensions will be removed (after the channel
-                has been moved to the end). So if input is `(H,W,D,C)` and C==1, then it will be saved as `(H,W,D)`.
-                If D is also 1, it will be saved as `(H,W)`. If ``False``, image will always be saved as `(H,W,D,C)`.
+                has been moved to the end). So if input is `(W,H,D,C)` and C==1, then it will be saved as `(W,H,D)`.
+                If D is also 1, it will be saved as `(W,H)`. If ``False``, image will always be saved as `(W,H,D,C)`.
             spatial_ndim: modifying the spatial dims if needed, so that output to have at least
                 this number of spatial dims. If ``None``, the output will have the same number of
                 spatial dimensions as the input.

monai/handlers/tensorboard_handlers.py

@@ -288,8 +288,8 @@ def _default_iteration_writer(self, engine: Engine, writer: SummaryWriter | Summ
 class TensorBoardImageHandler(TensorBoardHandler):
     """
     TensorBoardImageHandler is an Ignite Event handler that can visualize images, labels and outputs as 2D/3D images.
-    2D output (shape in Batch, channel, H, W) will be shown as simple image using the first element in the batch,
-    for 3D to ND output (shape in Batch, channel, H, W, D) input, each of ``self.max_channels`` number of images'
+    2D output (shape in Batch, channel, W, H) will be shown as simple image using the first element in the batch,
+    for 3D to ND output (shape in Batch, channel, W, H, D) input, each of ``self.max_channels`` number of images'
     last three dimensions will be shown as animated GIF along the last axis (typically Depth).
     And if writer is from TensorBoardX, data has 3 channels and `max_channels=3`, will plot as RGB video.
 
@@ -350,7 +350,7 @@ def __init__(
             index: plot which element in a data batch, default is the first element.
             max_channels: number of channels to plot.
             frame_dim: if plotting 3D image as GIF, specify the dimension used as frames,
-                expect input data shape as `NCHWD`, default to `-3` (the first spatial dim)
+                expect input data shape as `NCWHD`, default to `-3` (the first spatial dim)
             max_frames: if plot 3D RGB image as video in TensorBoardX, set the FPS to `max_frames`.
         """
         super().__init__(summary_writer=summary_writer, log_dir=log_dir)

monai/visualize/img2tensorboard.py

@@ -50,14 +50,16 @@ def _image3_animated_gif(
 
     Args:
         tag: Data identifier
-        image: 3D image tensors expected to be in `HWD` format
+        image: 3D image tensors expected to be in `WHD` format (axis 0 is
+            columns/Width, axis 1 is rows/Height, axis 2 is Depth, matching
+            arrays returned by MONAI's NIfTI/ITK readers).
         writer: the tensorboard writer to plot image
-        frame_dim: the dimension used as frames for GIF image, expect data shape as `HWD`, default to `0`.
+        frame_dim: the dimension used as frames for GIF image, expect data shape as `WHD`, default to `0`.
         scale_factor: amount to multiply values by. if the image data is between 0 and 1, using 255 for this value will
             scale it to displayable range
     """
     if len(image.shape) != 3:
-        raise AssertionError("3D image tensors expected to be in `HWD` format, len(image.shape) != 3")
+        raise AssertionError("3D image tensors expected to be in `WHD` format, len(image.shape) != 3")
 
     image_np, *_ = convert_data_type(image, output_type=np.ndarray)
     ims = [(i * scale_factor).astype(np.uint8, copy=False) for i in np.moveaxis(image_np, frame_dim, 0)]
@@ -85,14 +87,15 @@ def make_animated_gif_summary(
     frame_dim: int = -3,
     scale_factor: float = 1.0,
 ) -> Summary:
-    """Creates an animated gif out of an image tensor in 'CHWD' format and returns Summary.
+    """Creates an animated gif out of an image tensor in 'CWHD' format and returns Summary.
 
     Args:
         tag: Data identifier
-        image: The image, expected to be in `CHWD` format
+        image: The image, expected to be in `CWHD` format (channel-first; spatial axes are
+            Width, Height, Depth, matching arrays returned by MONAI's NIfTI/ITK readers).
         writer: the tensorboard writer to plot image
         max_out: maximum number of image channels to animate through
-        frame_dim: the dimension used as frames for GIF image, expect input data shape as `CHWD`,
+        frame_dim: the dimension used as frames for GIF image, expect input data shape as `CWHD`,
             default to `-3` (the first spatial dim)
         scale_factor: amount to multiply values by.
             if the image data is between 0 and 1, using 255 for this value will scale it to displayable range
@@ -122,14 +125,16 @@ def add_animated_gif(
     scale_factor: float = 1.0,
     global_step: int | None = None,
 ) -> None:
-    """Creates an animated gif out of an image tensor in 'CHWD' format and writes it with SummaryWriter.
+    """Creates an animated gif out of an image tensor in 'CWHD' format and writes it with SummaryWriter.
 
     Args:
         writer: Tensorboard SummaryWriter to write to
         tag: Data identifier
-        image_tensor: tensor for the image to add, expected to be in `CHWD` format
+        image_tensor: tensor for the image to add, expected to be in `CWHD` format (channel-first;
+            spatial axes are Width, Height, Depth, matching arrays returned by MONAI's
+            NIfTI/ITK readers).
         max_out: maximum number of image channels to animate through
-        frame_dim: the dimension used as frames for GIF image, expect input data shape as `CHWD`,
+        frame_dim: the dimension used as frames for GIF image, expect input data shape as `CWHD`,
             default to `-3` (the first spatial dim)
         scale_factor: amount to multiply values by. If the image data is between 0 and 1, using 255 for this value will
             scale it to displayable range
@@ -168,7 +173,7 @@ def plot_2d_or_3d_image(
         index: plot which element in the input data batch, default is the first element.
         max_channels: number of channels to plot.
         frame_dim: if plotting 3D image as GIF, specify the dimension used as frames,
-            expect input data shape as `NCHWD`, default to `-3` (the first spatial dim)
+            expect input data shape as `NCWHD`, default to `-3` (the first spatial dim)
         max_frames: if plot 3D RGB image as video in TensorBoardX, set the FPS to `max_frames`.
         tag: tag of the plotted image on TensorBoard.
     """

monai/visualize/utils.py

@@ -53,19 +53,24 @@ def matshow3d(
     Create a 3D volume figure as a grid of images.
 
     Args:
-        volume: 3D volume to display. data shape can be `BCHWD`, `CHWD` or `HWD`.
-            Higher dimensional arrays will be reshaped into (-1, H, W, [C]), `C` depends on `channel_dim` arg.
-            A list of channel-first (C, H[, W, D]) arrays can also be passed in,
+        volume: 3D volume to display. data shape can be `BCWHD`, `CWHD` or `WHD`
+            (axis 0 is columns/Width, axis 1 is rows/Height, axis 2 is Depth, matching
+            arrays returned by MONAI's NIfTI/ITK readers).
+            Higher dimensional arrays will be reshaped into (-1, spatial0, spatial1, [C]),
+            `C` depends on `channel_dim` arg.
+            A list of channel-first (C, W[, H, D]) arrays can also be passed in,
             in which case they will be displayed as a padded and stacked volume.
         fig: matplotlib figure or Axes to use. If None, a new figure will be created.
         title: title of the figure.
         figsize: size of the figure.
         frames_per_row: number of frames to display in each row. If None, sqrt(firstdim) will be used.
         frame_dim: for higher dimensional arrays, which dimension from (`-1`, `-2`, `-3`) is moved to
-            the `-3` dimension. dim and reshape to (-1, H, W) shape to construct frames, default to `-3`.
+            the `-3` dimension, then reshaped to (-1, spatial0, spatial1) to construct frames,
+            default to `-3`.
         channel_dim: if not None, explicitly specify the channel dimension to be transposed to the
-            last dimensionas shape (-1, H, W, C). this can be used to plot RGB color image.
-            if None, the channel dimension will be flattened with `frame_dim` and `batch_dim` as shape (-1, H, W).
+            last dimension as shape (-1, spatial0, spatial1, C). this can be used to plot RGB color image.
+            if None, the channel dimension will be flattened with `frame_dim` and `batch_dim` as
+            shape (-1, spatial0, spatial1).
             note that it can only support 3D input image. default is None.
         vmin: `vmin` for the matplotlib `imshow`.
         vmax: `vmax` for the matplotlib `imshow`.