add uncertainty, 1 ch saliency, separated datafile

bugfix

undo unexecpted changes

modify summary format

bugfix

fix CI problem

enhance comment

fix comment typo

use mindspore.log for errors

fix pylint issues

mindspore/ccsrc/utils/summary.proto

@@ -109,12 +109,18 @@ message Explain {
         repeated float ground_truth_prob = 1;
         repeated int32 predicted_label = 2;
         repeated float predicted_prob = 3;
+        repeated float ground_truth_prob_sd = 4;
+        repeated float ground_truth_prob_itl95_low = 5;
+        repeated float ground_truth_prob_itl95_hi = 6;
+        repeated float predicted_prob_sd = 7;
+        repeated float predicted_prob_itl95_low = 8;
+        repeated float predicted_prob_itl95_hi = 9;
     }
 
     message Explanation{
         optional string explain_method = 1;
         optional int32 label = 2;
-        optional bytes heatmap = 3;
+        optional string heatmap_path = 3;
 	}
 
     message Benchmark{
@@ -130,11 +136,10 @@ message Explain {
 		repeated string benchmark_method = 3;
 	}
 
-    optional string image_id = 1;  // The Metadata and image id and benchmark must have one fill in
-    optional bytes image_data = 2;
+    optional int32 sample_id = 1;
+    optional string image_path = 2;  // The Metadata and image path must have one fill in
     repeated int32 ground_truth_label = 3;
 
-
     optional Inference inference = 4;
     repeated Explanation explanation = 5;
     repeated Benchmark benchmark = 6;

mindspore/explainer/_runner.py

@@ -13,10 +13,15 @@
 # limitations under the License.
 # ============================================================================
 """Runner."""
+import os
+import re
+import traceback
 from time import time
 from typing import Tuple, List, Optional
 
 import numpy as np
+from scipy.stats import beta
+from PIL import Image
 
 from mindspore.train._utils import check_value_type
 from mindspore.train.summary_pb2 import Explain
@@ -24,34 +29,75 @@ import mindspore as ms
 import mindspore.dataset as ds
 from mindspore import log
 from mindspore.ops.operations import ExpandDims
-from mindspore.train.summary._summary_adapter import _convert_image_format, _make_image
+from mindspore.train.summary._summary_adapter import _convert_image_format
 from mindspore.train.summary.summary_record import SummaryRecord
+from mindspore.nn.probability.toolbox import UncertaintyEvaluation
 from .benchmark import Localization
 from .benchmark._attribution.metric import AttributionMetric
 from .explanation._attribution._attribution import Attribution
 
+# datafile directory names
+_DATAFILE_DIRNAME_PREFIX = "_explain_"
+_ORIGINAL_IMAGE_DIRNAME = "origin_images"
+_HEATMAP_DIRNAME = "heatmap"
+# max. no. of sample per directory
+_SAMPLE_PER_DIR = 1000
+
+
 _EXPAND_DIMS = ExpandDims()
-_CMAP_0 = np.reshape(np.array([55, 25, 86, 255]), [1, 1, 4]) / 255
-_CMAP_1 = np.reshape(np.array([255, 255, 0, 255]), [1, 1, 4]) / 255
 
 
 def _normalize(img_np):
-    """Normalize the image in the numpy array to be in [0, 255]. """
+    """Normalize the numpy image to the range of [0, 1]. """
     max_ = img_np.max()
     min_ = img_np.min()
     normed = (img_np - min_) / (max_ - min_).clip(min=1e-10)
-    return (normed * 255).astype(np.uint8)
+    return normed
+
+
+def _np_to_image(img_np, mode):
+    """Convert numpy array to PIL image."""
+    return Image.fromarray(np.uint8(img_np*255), mode=mode)
+
+
+def _calc_prob_interval(volume, probs, prob_vars):
+    """Compute the confidence interval of probability."""
+    if not isinstance(probs, np.ndarray):
+        probs = np.asarray(probs)
+    if not isinstance(prob_vars, np.ndarray):
+        prob_vars = np.asarray(prob_vars)
+    one_minus_probs = 1 - probs
+    alpha_coef = (np.square(probs) * one_minus_probs / prob_vars) - probs
+    beta_coef = alpha_coef * one_minus_probs / probs
+    intervals = beta.interval(volume, alpha_coef, beta_coef)
 
+    # avoid invalid result due to extreme small value of prob_vars
+    lows = []
+    highs = []
+    for i, low in enumerate(intervals[0]):
+        high = intervals[1][i]
+        if prob_vars[i] <= 0 or \
+                not np.isfinite(low) or low > probs[i] or \
+                not np.isfinite(high) or high < probs[i]:
+            low = probs[i]
+            high = probs[i]
+        lows.append(low)
+        highs.append(high)
 
-def _make_rgba(saliency):
-    """Make rgba image for saliency map."""
-    saliency = saliency.asnumpy().squeeze()
-    saliency = (saliency - saliency.min()) / (saliency.max() - saliency.min()).clip(1e-10)
-    rgba = np.empty((saliency.shape[0], saliency.shape[1], 4))
-    rgba[:, :, :] = np.expand_dims(saliency, 2)
-    rgba = rgba * _CMAP_1 + (1 - rgba) * _CMAP_0
-    rgba[:, :, -1] = saliency * 1
-    return rgba
+    return lows, highs
+
+
+def _get_id_dirname(sample_id: int):
+    """Get the name of parent directory of the image id."""
+    return str(int(sample_id/_SAMPLE_PER_DIR)*_SAMPLE_PER_DIR)
+
+
+def _extract_timestamp(filename: str):
+    """Extract timestamp from summary filename."""
+    matched = re.search(r"summary\.(\d+)", filename)
+    if matched:
+        return int(matched.group(1))
+    return None
 
 
 class ExplainRunner:
@@ -78,11 +124,14 @@ class ExplainRunner:
         self._count = 0
         self._classes = None
         self._model = None
+        self._uncertainty = None
+        self._summary_timestamp = None
 
     def run(self,
             dataset: Tuple,
             explainers: List,
-            benchmarkers: Optional[List] = None):
+            benchmarkers: Optional[List] = None,
+            uncertainty: Optional[UncertaintyEvaluation] = None):
         """
         Genereates results and writes results into the summary files in `summary_dir` specified during the object
         initialization.
@@ -98,7 +147,8 @@ class ExplainRunner:
                 `mindspore.explainer.explanation`.
             benchmarkers (list[Benchmark], optional): A list of benchmark objects to generate evaluation results.
                 Default: None
-
+            uncertainty (UncertaintyEvaluation, optional): An uncertainty evaluation object to evaluate the inference
+                uncertainty of samples.
         Examples:
             >>> from mindspore.explainer.explanation import GuidedBackprop, Gradient
             >>> # obtain dataset object
@@ -145,15 +195,31 @@ class ExplainRunner:
         inputs, _, _ = self._unpack_next_element(next_element)
         prop_test = self._model(inputs)
         check_value_type("output of model im explainer", prop_test, ms.Tensor)
-        if prop_test.shape[1] > len(self._classes):
-            raise ValueError("The dimension of model output should not exceed the length of dataset classes. Please "
+        if prop_test.shape[1] != len(self._classes):
+            raise ValueError("The dimension of model output does not match the length of dataset classes. Please "
                              "check dataset classes or the black-box model in the explainer again.")
 
+        if uncertainty is not None:
+            check_value_type("uncertainty", uncertainty, UncertaintyEvaluation)
+            prop_var_test = uncertainty.eval_epistemic_uncertainty(inputs)
+            check_value_type("output of uncertainty", prop_var_test, np.ndarray)
+            if prop_var_test.shape[1] != len(self._classes):
+                raise ValueError("The dimension of uncertainty output does not match the length of dataset classes"
+                                 "classes. Please check dataset classes or the black-box model in the explainer again.")
+            self._uncertainty = uncertainty
+        else:
+            self._uncertainty = None
+
         with SummaryRecord(self._summary_dir) as summary:
             print("Start running and writing......")
             begin = time()
             print("Start writing metadata.")
 
+            self._summary_timestamp = _extract_timestamp(summary.event_file_name)
+            if self._summary_timestamp is None:
+                raise RuntimeError("Cannot extract timestamp from summary filename!"
+                                   " It should contains a timestamp of 10 digits.")
+
             explain = Explain()
             explain.metadata.label.extend(classes)
             exp_names = [exp.__class__.__name__ for exp in explainers]
@@ -341,7 +407,7 @@ class ExplainRunner:
             bboxes = None
         else:
             inputs = next_element[0]
-            labels = [[] for x in inputs]
+            labels = [[] for _ in inputs]
             bboxes = None
         inputs, labels, bboxes = self._transform_data(inputs, labels, bboxes, ifbbox)
         return inputs, labels, bboxes
@@ -359,7 +425,7 @@ class ExplainRunner:
             2D Tensor.
         """
 
-        max_len = max([len(l) for l in labels])
+        max_len = max([len(label) for label in labels])
         batch_labels = np.zeros((len(labels), max_len))
 
         for idx, _ in enumerate(batch_labels):
@@ -368,7 +434,7 @@ class ExplainRunner:
 
         return ms.Tensor(batch_labels, ms.int32)
 
-    def _run_inference(self, dataset, summary, threshod=0.5):
+    def _run_inference(self, dataset, summary, threshold=0.5):
         """
         Run inference for the dataset and write the inference related data into summary.
 
@@ -387,30 +453,64 @@ class ExplainRunner:
             now = time()
             inputs, labels, _ = self._unpack_next_element(next_element)
             prob = self._model(inputs).asnumpy()
+            if self._uncertainty is not None:
+                prob_var = self._uncertainty.eval_epistemic_uncertainty(inputs)
+                prob_sd = np.sqrt(prob_var)
+            else:
+                prob_var = prob_sd = None
+
             for idx, inp in enumerate(inputs):
                 gt_labels = labels[idx]
                 gt_probs = [float(prob[idx][i]) for i in gt_labels]
 
                 data_np = _convert_image_format(np.expand_dims(inp.asnumpy(), 0), 'NCHW')
-                _, _, _, image_string = _make_image(_normalize(data_np))
+                original_image = _np_to_image(_normalize(data_np), mode='RGB')
+                original_image_path = self._save_original_image(self._count, original_image)
 
-                predicted_labels = [int(i) for i in (prob[idx] > threshod).nonzero()[0]]
+                predicted_labels = [int(i) for i in (prob[idx] > threshold).nonzero()[0]]
                 predicted_probs = [float(prob[idx][i]) for i in predicted_labels]
 
+                has_uncertainty = False
+                gt_prob_sds = gt_prob_itl95_lows = gt_prob_itl95_his = None
+                predicted_prob_sds = predicted_prob_itl95_lows = predicted_prob_itl95_his = None
+                if prob_var is not None:
+                    gt_prob_sds = [float(prob_sd[idx][i]) for i in gt_labels]
+                    predicted_prob_sds = [float(prob_sd[idx][i]) for i in predicted_labels]
+                    try:
+                        gt_prob_itl95_lows, gt_prob_itl95_his = \
+                            _calc_prob_interval(0.95, gt_probs, [float(prob_var[idx][i]) for i in gt_labels])
+                        predicted_prob_itl95_lows, predicted_prob_itl95_his = \
+                            _calc_prob_interval(0.95, predicted_probs, [float(prob_var[idx][i])
+                                                                        for i in predicted_labels])
+                        has_uncertainty = True
+                    except ValueError:
+                        log.error(traceback.format_exc())
+                        log.error("Error on calculating uncertainty")
+
                 union_labs = list(set(gt_labels + predicted_labels))
                 imageid_labels[str(self._count)] = union_labs
 
                 explain = Explain()
-                explain.image_id = str(self._count)
-                explain.image_data = image_string
-                summary.add_value("explainer", "image", explain)
+                explain.sample_id = self._count
+                explain.image_path = original_image_path
+                summary.add_value("explainer", "sample", explain)
 
                 explain = Explain()
-                explain.image_id = str(self._count)
+                explain.sample_id = self._count
                 explain.ground_truth_label.extend(gt_labels)
                 explain.inference.ground_truth_prob.extend(gt_probs)
                 explain.inference.predicted_label.extend(predicted_labels)
                 explain.inference.predicted_prob.extend(predicted_probs)
+
+                if has_uncertainty:
+                    explain.inference.ground_truth_prob_sd.extend(gt_prob_sds)
+                    explain.inference.ground_truth_prob_itl95_low.extend(gt_prob_itl95_lows)
+                    explain.inference.ground_truth_prob_itl95_hi.extend(gt_prob_itl95_his)
+
+                    explain.inference.predicted_prob_sd.extend(predicted_prob_sds)
+                    explain.inference.predicted_prob_itl95_low.extend(predicted_prob_itl95_lows)
+                    explain.inference.predicted_prob_itl95_hi.extend(predicted_prob_itl95_his)
+
                 summary.add_value("explainer", "inference", explain)
 
                 summary.record(1)
@@ -451,20 +551,20 @@ class ExplainRunner:
         for idx, union in enumerate(unions):
             saliency_dict = {}
             explain = Explain()
-            explain.image_id = str(self._count)
+            explain.sample_id = self._count
             for k, lab in enumerate(union):
                 saliency = batch_saliency_full[k][idx:idx + 1]
 
                 saliency_dict[lab] = saliency
 
-                saliency_np = _make_rgba(saliency)
-                _, _, _, saliency_string = _make_image(_normalize(saliency_np))
+                saliency_np = _normalize(saliency.asnumpy().squeeze())
+                saliency_image = _np_to_image(saliency_np, mode='L')
+                heatmap_path = self._save_heatmap(explainer.__class__.__name__, lab, self._count, saliency_image)
 
                 explanation = explain.explanation.add()
                 explanation.explain_method = explainer.__class__.__name__
-
+                explanation.heatmap_path = heatmap_path
                 explanation.label = lab
-                explanation.heatmap = saliency_string
 
             summary.add_value("explainer", "explanation", explain)
             summary.record(1)
@@ -496,3 +596,30 @@ class ExplainRunner:
                 else:
                     res = benchmarker.evaluate(explainer, inp, targets=label, saliency=saliency)
                     benchmarker.aggregate(res, label)
+
+    def _save_original_image(self, sample_id: int, image):
+        """Save an image to summary directory."""
+        id_dirname = _get_id_dirname(sample_id)
+        relative_dir = os.path.join(_DATAFILE_DIRNAME_PREFIX+str(self._summary_timestamp),
+                                    _ORIGINAL_IMAGE_DIRNAME,
+                                    id_dirname)
+        os.makedirs(os.path.join(self._summary_dir, relative_dir), exist_ok=True)
+        relative_path = os.path.join(relative_dir, f"{sample_id}.jpg")
+        save_path = os.path.join(self._summary_dir, relative_path)
+        with open(save_path, "wb") as file:
+            image.save(file)
+        return relative_path
+
+    def _save_heatmap(self, explain_method: str, class_id: int, sample_id: int, image):
+        """Save heatmap image to summary directory."""
+        id_dirname = _get_id_dirname(sample_id)
+        relative_dir = os.path.join(_DATAFILE_DIRNAME_PREFIX+str(self._summary_timestamp),
+                                    _HEATMAP_DIRNAME,
+                                    explain_method,
+                                    id_dirname)
+        os.makedirs(os.path.join(self._summary_dir, relative_dir), exist_ok=True)
+        relative_path = os.path.join(relative_dir, f"{sample_id}_{class_id}.jpg")
+        save_path = os.path.join(self._summary_dir, relative_path)
+        with open(save_path, "wb") as file:
+            image.save(file, optimize=True)
+        return relative_path

mindspore/train/summary/_explain_adapter.py

@@ -28,8 +28,8 @@ def check_explain_proto(explain):
     if not isinstance(explain, Explain):
         raise TypeError(f'Plugin explainer expects a {Explain.__name__} value.')
 
-    if not explain.image_id and not explain.metadata.label and not explain.benchmark:
-        raise ValueError(f'The Metadata and image id and benchmark must have one fill in.')
+    if not explain.image_path and not explain.inference and not explain.metadata.label and not explain.benchmark:
+        raise ValueError('One of metadata, image path, inference or benchmark has to be filled in.')
 
 
 def package_explain_event(explain_str):