!13879 change unet postprocess

From: @zhao_ting_v
Reviewed-by: @wuxuejian,@c_34
Signed-off-by: @c_34

model_zoo/official/cv/unet/eval.py

@@ -16,41 +16,30 @@
 import os
 import argparse
 import logging
+import cv2
 import numpy as np
-import mindspore
 import mindspore.nn as nn
 import mindspore.ops.operations as F
 from mindspore import context, Model
 from mindspore.train.serialization import load_checkpoint, load_param_into_net
-from mindspore.nn.loss.loss import _Loss
 
 from src.data_loader import create_dataset, create_cell_nuclei_dataset
 from src.unet_medical import UNetMedical
 from src.unet_nested import NestedUNet, UNet
 from src.config import cfg_unet
-
+from src.utils import UnetEval
-from scipy.special import softmax
 
 device_id = int(os.getenv('DEVICE_ID'))
 context.set_context(mode=context.GRAPH_MODE, device_target="Ascend", save_graphs=False, device_id=device_id)
 
 
-class CrossEntropyWithLogits(_Loss):
+class TempLoss(nn.Cell):
+    """A temp loss cell."""
     def __init__(self):
-        super(CrossEntropyWithLogits, self).__init__()
+        super(TempLoss, self).__init__()
-        self.transpose_fn = F.Transpose()
+        self.identity = F.identity()
-        self.reshape_fn = F.Reshape()
-        self.softmax_cross_entropy_loss = nn.SoftmaxCrossEntropyWithLogits()
-        self.cast = F.Cast()
     def construct(self, logits, label):
-        # NCHW->NHWC
+        return self.identity(logits)
-        logits = self.transpose_fn(logits, (0, 2, 3, 1))
-        logits = self.cast(logits, mindspore.float32)
-        label = self.transpose_fn(label, (0, 2, 3, 1))
-
-        loss = self.reduce_mean(self.softmax_cross_entropy_loss(self.reshape_fn(logits, (-1, 2)),
-                                                                self.reshape_fn(label, (-1, 2))))
-        return self.get_loss(loss)
 
 
 class dice_coeff(nn.Metric):
@@ -64,16 +53,35 @@ class dice_coeff(nn.Metric):
 
     def update(self, *inputs):
         if len(inputs) != 2:
-            raise ValueError('Mean dice coefficient need 2 inputs (y_pred, y), but got {}'.format(len(inputs)))
+            raise ValueError('Need 2 inputs ((y_softmax, y_argmax), y), but got {}'.format(len(inputs)))
-
-        y_pred = self._convert_data(inputs[0])
         y = self._convert_data(inputs[1])
-
         self._samples_num += y.shape[0]
-        y_pred = y_pred.transpose(0, 2, 3, 1)
         y = y.transpose(0, 2, 3, 1)
-        y_pred = softmax(y_pred, axis=3)
+        b, h, w, c = y.shape
-
+        if b != 1:
+            raise ValueError('Batch size should be 1 when in evaluation.')
+        y = y.reshape((h, w, c))
+        if cfg_unet["eval_activate"].lower() == "softmax":
+            y_softmax = np.squeeze(self._convert_data(inputs[0][0]), axis=0)
+            if cfg_unet["eval_resize"]:
+                y_pred = []
+                for i in range(cfg_unet["num_classes"]):
+                    y_pred.append(cv2.resize(np.uint8(y_softmax[:, :, i] * 255), (w, h)) / 255)
+                y_pred = np.stack(y_pred, axis=-1)
+            else:
+                y_pred = y_softmax
+        elif cfg_unet["eval_activate"].lower() == "argmax":
+            y_argmax = np.squeeze(self._convert_data(inputs[0][1]), axis=0)
+            y_pred = []
+            for i in range(cfg_unet["num_classes"]):
+                if cfg_unet["eval_resize"]:
+                    y_pred.append(cv2.resize(np.uint8(y_argmax == i), (w, h), interpolation=cv2.INTER_NEAREST))
+                else:
+                    y_pred.append(np.float32(y_argmax == i))
+            y_pred = np.stack(y_pred, axis=-1)
+        else:
+            raise ValueError('config eval_activate should be softmax or argmax.')
+        y_pred = y_pred.astype(np.float32)
         inter = np.dot(y_pred.flatten(), y.flatten())
         union = np.dot(y_pred.flatten(), y_pred.flatten()) + np.dot(y.flatten(), y.flatten())
 
@@ -104,14 +112,14 @@ def test_net(data_dir,
         raise ValueError("Unsupported model: {}".format(cfg['model']))
     param_dict = load_checkpoint(ckpt_path)
     load_param_into_net(net, param_dict)
-
+    net = UnetEval(net)
-    criterion = CrossEntropyWithLogits()
     if 'dataset' in cfg and cfg['dataset'] == "Cell_nuclei":
-        valid_dataset = create_cell_nuclei_dataset(data_dir, cfg['img_size'], 1, 1, is_train=False, split=0.8)
+        valid_dataset = create_cell_nuclei_dataset(data_dir, cfg['img_size'], 1, 1, is_train=False,
+                                                   eval_resize=cfg["eval_resize"], split=0.8)
     else:
         _, valid_dataset = create_dataset(data_dir, 1, 1, False, cross_valid_ind, False,
                                           do_crop=cfg['crop'], img_size=cfg['img_size'])
-    model = Model(net, loss_fn=criterion, metrics={"dice_coeff": dice_coeff()})
+    model = Model(net, loss_fn=TempLoss(), metrics={"dice_coeff": dice_coeff()})
 
     print("============== Starting Evaluating ============")
     eval_score = model.eval(valid_dataset, dataset_sink_mode=False)["dice_coeff"]

model_zoo/official/cv/unet/src/config.py

@@ -33,7 +33,9 @@ cfg_unet_medical = {
     'resume': False,
     'resume_ckpt': './',
     'transfer_training': False,
-    'filter_weight': ['outc.weight', 'outc.bias']
+    'filter_weight': ['outc.weight', 'outc.bias'],
+    'eval_activate': 'Softmax',
+    'eval_resize': False
 }
 
 cfg_unet_nested = {
@@ -59,7 +61,9 @@ cfg_unet_nested = {
     'resume': False,
     'resume_ckpt': './',
     'transfer_training': False,
-    'filter_weight': ['final1.weight', 'final2.weight', 'final3.weight', 'final4.weight']
+    'filter_weight': ['final1.weight', 'final2.weight', 'final3.weight', 'final4.weight'],
+    'eval_activate': 'Softmax',
+    'eval_resize': False
 }
 
 cfg_unet_nested_cell = {
@@ -86,7 +90,9 @@ cfg_unet_nested_cell = {
     'resume': False,
     'resume_ckpt': './',
     'transfer_training': False,
-    'filter_weight': ['final1.weight', 'final2.weight', 'final3.weight', 'final4.weight']
+    'filter_weight': ['final1.weight', 'final2.weight', 'final3.weight', 'final4.weight'],
+    'eval_activate': 'Softmax',
+    'eval_resize': False
 }
 
 cfg_unet_simple = {
@@ -109,7 +115,12 @@ cfg_unet_simple = {
     'resume': False,
     'resume_ckpt': './',
     'transfer_training': False,
-    'filter_weight': ["final.weight"]
+    'filter_weight': ["final.weight"],
+    'eval_activate': 'Softmax',
+    'eval_resize': False
 }
 
 cfg_unet = cfg_unet_medical
+if not ('dataset' in cfg_unet and cfg_unet['dataset'] == 'Cell_nuclei') and cfg_unet['eval_resize']:
+    print("ISBI dataset not support resize to original image size when in evaluation.")
+    cfg_unet['eval_resize'] = False

model_zoo/official/cv/unet/src/data_loader.py

@@ -216,7 +216,7 @@ class CellNucleiDataset:
             return len(self.train_ids)
         return len(self.val_ids)
 
-def preprocess_img_mask(img, mask, img_size, augment=False):
+def preprocess_img_mask(img, mask, img_size, augment=False, eval_resize=False):
     """
     Preprocess for cell nuclei dataset.
     Random crop and flip images and masks when augment is True.
@@ -236,7 +236,8 @@ def preprocess_img_mask(img, mask, img_size, augment=False):
             mask = cv2.flip(mask, flip_code)
     else:
         img = cv2.resize(img, img_size)
-        mask = cv2.resize(mask, img_size)
+        if not eval_resize:
+            mask = cv2.resize(mask, img_size)
     img = (img.astype(np.float32) - 127.5) / 127.5
     img = img.transpose(2, 0, 1)
     mask = mask.astype(np.float32) / 255
@@ -245,7 +246,7 @@ def preprocess_img_mask(img, mask, img_size, augment=False):
     mask = mask.transpose(2, 0, 1).astype(np.float32)
     return img, mask
 
-def create_cell_nuclei_dataset(data_dir, img_size, repeat, batch_size, is_train=False, augment=False,
+def create_cell_nuclei_dataset(data_dir, img_size, repeat, batch_size, is_train=False, augment=False, eval_resize=False,
                                split=0.8, rank=0, group_size=1, python_multiprocessing=True, num_parallel_workers=8):
     """
     Get generator dataset for cell nuclei dataset.
@@ -253,7 +254,8 @@ def create_cell_nuclei_dataset(data_dir, img_size, repeat, batch_size, is_train=
     cell_dataset = CellNucleiDataset(data_dir, repeat, is_train, split)
     sampler = ds.DistributedSampler(group_size, rank, shuffle=is_train)
     dataset = ds.GeneratorDataset(cell_dataset, cell_dataset.column_names, sampler=sampler)
-    compose_map_func = (lambda image, mask: preprocess_img_mask(image, mask, tuple(img_size), augment and is_train))
+    compose_map_func = (lambda image, mask: preprocess_img_mask(image, mask, tuple(img_size), augment and is_train,
+                                                                eval_resize))
     dataset = dataset.map(operations=compose_map_func, input_columns=cell_dataset.column_names,
                           output_columns=cell_dataset.column_names, column_order=cell_dataset.column_names,
                           python_multiprocessing=python_multiprocessing,

model_zoo/official/cv/unet/src/utils.py

@@ -16,9 +16,29 @@
 import time
 import numpy as np
 from PIL import Image
+from mindspore import nn
+from mindspore.ops import operations as ops
 from mindspore.train.callback import Callback
 from mindspore.common.tensor import Tensor
 
+class UnetEval(nn.Cell):
+    """
+    Add Unet evaluation activation.
+    """
+    def __init__(self, net):
+        super(UnetEval, self).__init__()
+        self.net = net
+        self.transpose = ops.Transpose()
+        self.softmax = ops.Softmax(axis=-1)
+        self.argmax = ops.Argmax(axis=-1)
+
+    def construct(self, x):
+        out = self.net(x)
+        out = self.transpose(out, (0, 2, 3, 1))
+        softmax_out = self.softmax(out)
+        argmax_out = self.argmax(out)
+        return (softmax_out, argmax_out)
+
 class StepLossTimeMonitor(Callback):
 
     def __init__(self, batch_size, per_print_times=1):