Support for MNIST dataset format (#234)

* add mnist format

* add mnist csv format

* add mnist to documentation

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Support for CIFAR-10/100 dataset format (<https://github.com/openvinotoolkit/datumaro/pull/225>)
 - Support COCO panoptic and stuff format (<https://github.com/openvinotoolkit/datumaro/pull/210>)
 - Documentation file and integration tests for Pascal VOC format (<https://github.com/openvinotoolkit/datumaro/pull/228>)
+- Support for MNIST and MNIST in CSV dataset formats (<https://github.com/openvinotoolkit/datumaro/pull/234>)
 
 ### Changed
 - LabelMe format saves dataset items with their relative paths by subsets without changing names (<https://github.com/openvinotoolkit/datumaro/pull/200>)

README.md

@@ -134,6 +134,8 @@ CVAT annotations                             ---> Publication, statistics etc.
   - [MOTS PNG](https://www.vision.rwth-aachen.de/page/mots)
   - [ImageNet](http://image-net.org/)
   - [CIFAR-10/100](https://www.cs.toronto.edu/~kriz/cifar.html) (`classification`)
+  - [MNIST](http://yann.lecun.com/exdb/mnist/) (`classification`)
+  - [MNIST in CSV](https://pjreddie.com/projects/mnist-in-csv/) (`classification`)
   - [CamVid](http://mi.eng.cam.ac.uk/research/projects/VideoRec/CamVid/)
   - [CVAT](https://github.com/opencv/cvat/blob/develop/cvat/apps/documentation/xml_format.md)
   - [LabelMe](http://labelme.csail.mit.edu/Release3.0)

datumaro/plugins/mnist_csv_format.py

@@ -0,0 +1,170 @@
+# Copyright (C) 2021 Intel Corporation
+#
+# SPDX-License-Identifier: MIT
+
+import os
+import os.path as osp
+
+import numpy as np
+from datumaro.components.converter import Converter
+from datumaro.components.extractor import (AnnotationType, DatasetItem,
+    Importer, Label, LabelCategories, SourceExtractor)
+
+
+class MnistCsvPath:
+    IMAGE_SIZE = 28
+    NONE_LABEL = -1
+
+class MnistCsvExtractor(SourceExtractor):
+    def __init__(self, path, subset=None):
+        if not osp.isfile(path):
+            raise FileNotFoundError("Can't read annotation file '%s'" % path)
+
+        if not subset:
+            file_name = osp.splitext(osp.basename(path))[0]
+            subset = file_name.rsplit('_', maxsplit=1)[-1]
+
+        super().__init__(subset=subset)
+        self._dataset_dir = osp.dirname(path)
+
+        self._categories = self._load_categories()
+
+        self._items = list(self._load_items(path).values())
+
+    def _load_categories(self):
+        label_cat = LabelCategories()
+
+        labels_file = osp.join(self._dataset_dir, 'labels.txt')
+        if osp.isfile(labels_file):
+            with open(labels_file, encoding='utf-8') as f:
+                for line in f:
+                    line = line.strip()
+                    if not line:
+                        continue
+                    label_cat.add(line)
+        else:
+            for i in range(10):
+                label_cat.add(str(i))
+
+        return { AnnotationType.label: label_cat }
+
+    def _load_items(self, path):
+        items = {}
+        with open(path, 'r', encoding='utf-8') as f:
+            annotation_table = f.readlines()
+
+        metafile = osp.join(self._dataset_dir, 'meta_%s.csv' % self._subset)
+        meta = []
+        if osp.isfile(metafile):
+            with open(metafile, 'r', encoding='utf-8') as f:
+                meta = f.readlines()
+
+        for i, data in enumerate(annotation_table):
+            data = data.split(',')
+            item_anno = []
+            label = int(data[0])
+            if label != MnistCsvPath.NONE_LABEL:
+                item_anno.append(Label(label))
+
+            if 0 < len(meta):
+                meta[i] = meta[i].strip().split(',')
+
+            # support for single-channel image only
+            image = None
+            if 1 < len(data):
+                if 0 < len(meta) and 1 < len(meta[i]):
+                    image = np.array([int(pix) for pix in data[1:]],
+                        dtype='uint8').reshape(int(meta[i][-2]), int(meta[i][-1]))
+                else:
+                    image = np.array([int(pix) for pix in data[1:]],
+                        dtype='uint8').reshape(28, 28)
+
+            if 0 < len(meta) and len(meta[i]) in [1, 3]:
+                i = meta[i][0]
+
+            items[i] = DatasetItem(id=i, subset=self._subset,
+                image=image, annotations=item_anno)
+        return items
+
+class MnistCsvImporter(Importer):
+    @classmethod
+    def find_sources(cls, path):
+        return cls._find_sources_recursive(path, '.csv', 'mnist_csv',
+            file_filter=lambda p: not osp.basename(p).startswith('meta'))
+
+class MnistCsvConverter(Converter):
+    DEFAULT_IMAGE_EXT = '.png'
+
+    def apply(self):
+        os.makedirs(self._save_dir, exist_ok=True)
+        for subset_name, subset in self._extractor.subsets().items():
+            data = []
+            item_ids = {}
+            image_sizes = {}
+            for item in subset:
+                anns = [a.label for a in item.annotations
+                    if a.type == AnnotationType.label]
+                label = MnistCsvPath.NONE_LABEL
+                if anns:
+                    label = anns[0]
+
+                if item.has_image and self._save_images:
+                    image = item.image
+                    if not image.has_data:
+                        data.append([label, None])
+                    else:
+                        if image.data.shape[0] != MnistCsvPath.IMAGE_SIZE or \
+                                image.data.shape[1] != MnistCsvPath.IMAGE_SIZE:
+                            image_sizes[len(data)] = [image.data.shape[0],
+                                image.data.shape[1]]
+                        image = image.data.reshape(-1).astype(np.uint8).tolist()
+                        image.insert(0, label)
+                        data.append(image)
+                else:
+                    data.append([label])
+
+                if item.id != str(len(data) - 1):
+                    item_ids[len(data) - 1] = item.id
+
+            anno_file = osp.join(self._save_dir, 'mnist_%s.csv' % subset_name)
+            self.save_in_csv(anno_file, data)
+
+            # it is't in the original format,
+            # this is for storng other names and sizes of images
+            if len(item_ids) or len(image_sizes):
+                meta = []
+                if len(item_ids) and len(image_sizes):
+                    # other names and sizes of images
+                    size = [MnistCsvPath.IMAGE_SIZE, MnistCsvPath.IMAGE_SIZE]
+                    for i in range(len(data)):
+                        w, h = image_sizes.get(i, size)
+                        meta.append([item_ids.get(i, i), w, h])
+
+                elif len(item_ids):
+                    # other names of images
+                    for i in range(len(data)):
+                        meta.append([item_ids.get(i, i)])
+
+                elif len(image_sizes):
+                    # other sizes of images
+                    size = [MnistCsvPath.IMAGE_SIZE, MnistCsvPath.IMAGE_SIZE]
+                    for i in range(len(data)):
+                        meta.append(image_sizes.get(i, size))
+
+                metafile = osp.join(self._save_dir, 'meta_%s.csv' % subset_name)
+                self.save_in_csv(metafile, meta)
+
+        self.save_labels()
+
+    def save_in_csv(self, path, data):
+        with open(path, 'w', encoding='utf-8') as f:
+            for row in data:
+                f.write(','.join([str(p) for p in row]) + "\n")
+
+    def save_labels(self):
+        labels_file = osp.join(self._save_dir, 'labels.txt')
+        with open(labels_file, 'w', encoding='utf-8') as f:
+            f.writelines(l.name + '\n'
+                for l in self._extractor.categories().get(
+                    AnnotationType.label, LabelCategories())
+            )

datumaro/plugins/mnist_format.py

@@ -0,0 +1,209 @@
+# Copyright (C) 2021 Intel Corporation
+#
+# SPDX-License-Identifier: MIT
+
+import gzip
+import os
+import os.path as osp
+
+import numpy as np
+from datumaro.components.converter import Converter
+from datumaro.components.extractor import (AnnotationType, DatasetItem,
+    Importer, Label, LabelCategories, SourceExtractor)
+
+
+class MnistPath:
+    TEST_LABELS_FILE = 't10k-labels-idx1-ubyte.gz'
+    TEST_IMAGES_FILE = 't10k-images-idx3-ubyte.gz'
+    LABELS_FILE = '-labels-idx1-ubyte.gz'
+    IMAGES_FILE = '-images-idx3-ubyte.gz'
+    IMAGE_SIZE = 28
+    NONE_LABEL = 255
+
+class MnistExtractor(SourceExtractor):
+    def __init__(self, path, subset=None):
+        if not osp.isfile(path):
+            raise FileNotFoundError("Can't read annotation file '%s'" % path)
+
+        if not subset:
+            file_name = osp.splitext(osp.basename(path))[0]
+            if file_name.startswith('t10k'):
+                subset = 'test'
+            else:
+                subset = file_name.split('-', maxsplit=1)[0]
+
+        super().__init__(subset=subset)
+        self._dataset_dir = osp.dirname(path)
+
+        self._categories = self._load_categories()
+
+        self._items = list(self._load_items(path).values())
+
+    def _load_categories(self):
+        label_cat = LabelCategories()
+
+        labels_file = osp.join(self._dataset_dir, 'labels.txt')
+        if osp.isfile(labels_file):
+            with open(labels_file, encoding='utf-8') as f:
+                for line in f:
+                    line = line.strip()
+                    if not line:
+                        continue
+                    label_cat.add(line)
+        else:
+            for i in range(10):
+                label_cat.add(str(i))
+
+        return { AnnotationType.label: label_cat }
+
+    def _load_items(self, path):
+        items = {}
+        with gzip.open(path, 'rb') as lbpath:
+            labels = np.frombuffer(lbpath.read(), dtype=np.uint8, offset=8)
+
+        meta = []
+        metafile = osp.join(self._dataset_dir, self._subset + '-meta.gz')
+        if osp.isfile(metafile):
+            with gzip.open(metafile, 'rb') as f:
+                meta = np.frombuffer(f.read(), dtype='<U32')
+            meta = meta.reshape(len(labels), int(len(meta) / len(labels)))
+
+        # support for single-channel image only
+        images = None
+        images_file = osp.join(self._dataset_dir,
+            osp.basename(path).replace('labels-idx1', 'images-idx3'))
+        if osp.isfile(images_file):
+            with gzip.open(images_file, 'rb') as imgpath:
+                images = np.frombuffer(imgpath.read(), dtype=np.uint8, offset=16)
+                if len(meta) == 0 or len(meta[0]) < 2:
+                    images = images.reshape(len(labels), MnistPath.IMAGE_SIZE,
+                        MnistPath.IMAGE_SIZE)
+
+        pix_num = 0
+        for i, annotation in enumerate(labels):
+            annotations = []
+            label = annotation
+            if label != MnistPath.NONE_LABEL:
+                annotations.append(Label(label))
+
+            image = None
+            if images is not None:
+                if 0 < len(meta) and 1 < len(meta[i]):
+                    h, w = int(meta[i][-2]), int(meta[i][-1])
+                    image = images[pix_num : pix_num + h * w].reshape(h, w)
+                    pix_num += h * w
+                else:
+                    image = images[i].reshape(MnistPath.IMAGE_SIZE, MnistPath.IMAGE_SIZE)
+
+            if 0 < len(meta) and (len(meta[i]) == 1 or len(meta[i]) == 3):
+                i = meta[i][0]
+
+            items[i] = DatasetItem(id=i, subset=self._subset,
+                image=image, annotations=annotations)
+        return items
+
+class MnistImporter(Importer):
+    @classmethod
+    def find_sources(cls, path):
+        return cls._find_sources_recursive(path, '.gz', 'mnist',
+            file_filter=lambda p: osp.basename(p).split('-')[1] == 'labels')
+
+class MnistConverter(Converter):
+    DEFAULT_IMAGE_EXT = '.png'
+
+    def apply(self):
+        os.makedirs(self._save_dir, exist_ok=True)
+        for subset_name, subset in self._extractor.subsets().items():
+            labels = []
+            images = np.array([])
+            item_ids = {}
+            image_sizes = {}
+            for item in subset:
+                anns = [a.label for a in item.annotations
+                    if a.type == AnnotationType.label]
+                label = 255
+                if anns:
+                    label = anns[0]
+                labels.append(label)
+
+                if item.id != str(len(labels) - 1):
+                    item_ids[len(labels) - 1] = item.id
+
+                if item.has_image and self._save_images:
+                    image = item.image
+                    if not image.has_data:
+                        image_sizes[len(images) - 1] = [0, 0]
+                    else:
+                        image = image.data
+                        if image.shape[0] != MnistPath.IMAGE_SIZE or \
+                                image.shape[1] != MnistPath.IMAGE_SIZE:
+                            image_sizes[len(labels) - 1] = [image.shape[0], image.shape[1]]
+                        images = np.append(images, image.reshape(-1).astype(np.uint8))
+
+            if subset_name == 'test':
+                labels_file = osp.join(self._save_dir,
+                    MnistPath.TEST_LABELS_FILE)
+            else:
+                labels_file = osp.join(self._save_dir,
+                    subset_name + MnistPath.LABELS_FILE)
+            self.save_annotations(labels_file, labels)
+
+            if 0 < len(images):
+                if subset_name == 'test':
+                    images_file = osp.join(self._save_dir,
+                        MnistPath.TEST_IMAGES_FILE)
+                else:
+                    images_file = osp.join(self._save_dir,
+                        subset_name + MnistPath.IMAGES_FILE)
+                self.save_images(images_file, images)
+
+            # it is't in the original format,
+            # this is for storng other names and sizes of images
+            if len(item_ids) or len(image_sizes):
+                meta = []
+                if len(item_ids) and len(image_sizes):
+                    # other names and sizes of images
+                    size = [MnistPath.IMAGE_SIZE, MnistPath.IMAGE_SIZE]
+                    for i in range(len(labels)):
+                        w, h = image_sizes.get(i, size)
+                        meta.append([item_ids.get(i, i), w, h])
+
+                elif len(item_ids):
+                    # other names of images
+                    for i in range(len(labels)):
+                        meta.append([item_ids.get(i, i)])
+
+                elif len(image_sizes):
+                    # other sizes of images
+                    size = [MnistPath.IMAGE_SIZE, MnistPath.IMAGE_SIZE]
+                    for i in range(len(labels)):
+                        meta.append(image_sizes.get(i, size))
+
+                metafile = osp.join(self._save_dir, subset_name + '-meta.gz')
+                with gzip.open(metafile, 'wb') as f:
+                    f.write(np.array(meta, dtype='<U32').tobytes())
+
+        self.save_labels()
+
+    def save_annotations(self, path, data):
+        with gzip.open(path, 'wb') as f:
+            # magic number = 0x0801 (2049, hexadecimal representation)
+            # this is used to verify the file with MNIST mark data
+            f.write(np.array([0x0801, len(data)], dtype='>i4').tobytes())
+            f.write(np.array(data, dtype='uint8').tobytes())
+
+    def save_images(self, path, data):
+        with gzip.open(path, 'wb') as f:
+            # magic number = 0x0803 (2051, hexadecimal representation),
+            # this is used to verify the file with MNIST image data
+            f.write(np.array([0x0803, len(data), MnistPath.IMAGE_SIZE,
+                MnistPath.IMAGE_SIZE], dtype='>i4').tobytes())
+            f.write(np.array(data, dtype='uint8').tobytes())
+
+    def save_labels(self):
+        labels_file = osp.join(self._save_dir, 'labels.txt')
+        with open(labels_file, 'w', encoding='utf-8') as f:
+            f.writelines(l.name + '\n'
+                for l in self._extractor.categories().get(
+                    AnnotationType.label, LabelCategories())
+            )