def predict(
im_or_path: Union[np.ndarray, Union[str, Path]],
learn: Learner,
thres: float = None,
) -> [np.ndarray, np.ndarray]:
""" Run model inference.
Args:
im_or_path: image or path to image
learn: trained model
thres: threshold under which to reject predicted label and set to class-id 0 instead.
Return:
The predicted mask with pixel-wise confidence scores.
"""
im = load_im(im_or_path)
_, mask, scores = learn.predict(im, thresh=thres)
mask = np.array(mask).squeeze()
scores = np.array(scores)
# Fastai seems to ignore the confidance threshold 'thresh'. Hence here
# setting all predictions with low confidence to be 'background'.
if thres is not None:
max_scores = np.max(np.array(scores), axis=0)
mask[max_scores <= thres] = 0
return mask, scores
def compute_feature(im_or_path: Image, learn: Learner,
embedding_layer: Module) -> List[float]:
"""Compute features for a single image
Args:
im_or_path: Image or path to image
learn: Trained model to use as featurizer
embedding_layer: Number of columns on which to display the images
Returns: DNN feature of the provided image.
"""
if isinstance(im_or_path, str):
im = open_image(im_or_path, convert_mode="RGB")
else:
im = im_or_path
featurizer = SaveFeatures(embedding_layer)
featurizer.features = None
learn.predict(im)
feats = featurizer.features[0][:]
assert len(feats) > 1
featurizer.features = None
return feats
class YOLOv3(ArcGISModel):
"""
Creates a YOLOv3 object detector.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
data Required fastai Databunch. Returned data object from
`prepare_data` function.
--------------------- -------------------------------------------
pretrained_path Optional string. Path where pre-trained model is
saved.
===================== ===========================================
:returns: `YOLOv3` Object
"""
def __init__(self, data=None, pretrained_path=None, **kwargs):
if data is None:
data = create_coco_data()
else:
#Removing normalization because YOLO ingests images with values in range 0-1
data.remove_tfm(data.norm)
data.norm, data.denorm = None, None
super().__init__(data)
#Creating a dummy class for the backbone because this model does not use a torchvision backbone
class DarkNet53():
def __init__(self):
self.name = "DarkNet53"
self._backbone = DarkNet53
self._code = code
self._data = data
self.config_model = {}
if getattr(data, "_is_coco", "") == True:
self.config_model = coco_config()
else:
anchors = kwargs.get('anchors', None)
self.config_model[
'ANCHORS'] = anchors if anchors is not None else generate_anchors(
num_anchor=9, hw=data.height_width)
self.config_model['ANCH_MASK'] = [[6, 7, 8], [3, 4, 5], [0, 1, 2]]
self.config_model[
'N_CLASSES'] = data.c - 1 # Subtract 1 for the background class
n_bands = kwargs.get('n_bands', None)
self.config_model[
'N_BANDS'] = n_bands if n_bands is not None else data.x[
0].data.shape[0]
self._model = YOLOv3_Model(self.config_model)
pretrained = kwargs.get('pretrained_backbone', True)
if pretrained:
# Download (if required) and load YOLOv3 weights pretrained on COCO dataset
weights_path = os.path.join(Path.home(), '.cache', 'weights')
if not os.path.exists(weights_path): os.makedirs(weights_path)
weights_file = os.path.join(weights_path, 'yolov3.weights')
if not os.path.exists(weights_file):
try:
download_yolo_weights(weights_path)
extract_zipfile(weights_path, 'yolov3.zip', remove=True)
except Exception as e:
print(e)
print(
"[INFO] Can't download and extract COCO pretrained weights for YOLOv3.\nProceeding without pretrained weights."
)
if os.path.exists(weights_file):
parse_yolo_weights(self._model, weights_file)
from IPython.display import clear_output
clear_output()
self._loss_f = YOLOv3_Loss()
self.learn = Learner(data, self._model, loss_func=self._loss_f)
self.learn.split([self._model.module_list[11]
]) #Splitting the model at Darknet53 backbone
self.learn.freeze()
if pretrained_path is not None:
self.load(str(pretrained_path))
# make first conv weights learnable and use _show_results_multispectral when using multispectral data
self._arcgis_init_callback()
# Set a default flag to toggle appending labels with images before passing images through the model
self.learn.predicting = False
self.learn.callbacks.append(AppendLabelsCallback(self.learn))
def __str__(self):
return self.__repr__()
def __repr__(self):
return '<%s>' % (type(self).__name__)
@property
def supported_backbones(self):
""" Supported backbones for this model. """
return ['DarkNet53']
@property
def _model_metrics(self):
if getattr(self._data, "_is_coco", "") == True:
return {'accuracy': {'IoU': 0.50, 'AP': 0.558}}
return {'accuracy': self.average_precision_score(show_progress=False)}
def _analyze_pred(self,
pred,
thresh=0.1,
nms_overlap=0.1,
ret_scores=True,
device=None):
""" """
return postprocess(pred,
chip_size=self.learn.data.chip_size,
conf_thre=thresh,
nms_thre=nms_overlap)
def show_results(self, rows=5, thresh=0.1, nms_overlap=0.1):
"""
Displays the results of a trained model on a part of the validation set.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
rows Optional int. Number of rows of results
to be displayed.
--------------------- -------------------------------------------
thresh Optional float. The probabilty above which
a detection will be considered valid.
--------------------- -------------------------------------------
nms_overlap Optional float. The intersection over union
threshold with other predicted bounding
boxes, above which the box with the highest
score will be considered a true positive.
===================== ===========================================
"""
self._check_requisites()
if rows > len(self._data.valid_ds):
rows = len(self._data.valid_ds)
self.learn.predicting = True
self.learn.show_results(rows=rows,
thresh=thresh,
nms_overlap=nms_overlap,
model=self)
def _show_results_multispectral(self,
rows=5,
thresh=0.3,
nms_overlap=0.1,
alpha=1,
**kwargs):
self.learn.predicting = True
ax = show_results_multispectral(self,
nrows=rows,
thresh=thresh,
nms_overlap=nms_overlap,
alpha=alpha,
**kwargs)
def predict(self,
image_path,
threshold=0.1,
nms_overlap=0.1,
return_scores=True,
visualize=False,
resize=False):
"""
Predicts and displays the results of a trained model on a single image.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
image_path Required. Path to the image file to make the
predictions on.
--------------------- -------------------------------------------
thresh Optional float. The probabilty above which
a detection will be considered valid.
--------------------- -------------------------------------------
nms_overlap Optional float. The intersection over union
threshold with other predicted bounding
boxes, above which the box with the highest
score will be considered a true positive.
--------------------- -------------------------------------------
return_scores Optional boolean.
Will return the probability scores of the
bounding box predictions if True.
--------------------- -------------------------------------------
visualize Optional boolean. Displays the image with
predicted bounding boxes if True.
--------------------- -------------------------------------------
resize Optional boolean. Resizes the image to the same size
(chip_size parameter in prepare_data) that the model was trained on,
before detecting objects.
Note that if resize_to parameter was used in prepare_data,
the image is resized to that size instead.
By default, this parameter is false and the detections are run
in a sliding window fashion by applying the model on cropped sections
of the image (of the same size as the model was trained on).
===================== ===========================================
:returns: 'List' of xmin, ymin, width, height of predicted bounding boxes on the given image
"""
if not HAS_OPENCV:
raise Exception(
"This function requires opencv 4.0.1.24. Install it using pip install opencv-python==4.0.1.24"
)
if not HAS_PIL:
raise Exception(
"This function requires PIL. Please install it via pip or conda"
)
if isinstance(image_path, str):
image = cv2.imread(image_path)
else:
image = image_path
orig_height, orig_width, _ = image.shape
orig_frame = image.copy()
if resize and self._data.resize_to is None\
and self._data.chip_size is not None:
image = cv2.resize(image,
(self._data.chip_size, self._data.chip_size))
if self._data.resize_to is not None:
if isinstance(self._data.resize_to, tuple):
image = cv2.resize(image, self._data.resize_to)
else:
image = cv2.resize(
image, (self._data.resize_to, self._data.resize_to))
height, width, _ = image.shape
if self._data.chip_size is not None:
chips = _get_image_chips(image, self._data.chip_size)
else:
chips = [{
'width': width,
'height': height,
'xmin': 0,
'ymin': 0,
'chip': image,
'predictions': []
}]
valid_tfms = self._data.valid_ds.tfms
self._data.valid_ds.tfms = []
include_pad_detections = False
if len(chips) == 1:
include_pad_detections = True
for chip in chips:
frame = Image(
pil2tensor(PIL.Image.fromarray(
cv2.cvtColor(chip['chip'], cv2.COLOR_BGR2RGB)),
dtype=np.float32).div_(255))
self.learn.predicting = True
bbox = self.learn.predict(frame,
thresh=threshold,
nms_overlap=nms_overlap,
ret_scores=True,
model=self)[0]
if bbox:
scores = bbox.scores
bboxes, lbls = bbox._compute_boxes()
bboxes.add_(1).mul_(
torch.tensor([
chip['height'] / 2, chip['width'] / 2,
chip['height'] / 2, chip['width'] / 2
])).long()
for index, bbox in enumerate(bboxes):
if lbls is not None:
label = lbls[index]
else:
label = 'Default'
data = bb2hw(bbox)
if include_pad_detections or not _exclude_detection(
(data[0], data[1], data[2], data[3]), chip['width'],
chip['height']):
chip['predictions'].append({
'xmin':
data[0],
'ymin':
data[1],
'width':
data[2],
'height':
data[3],
'score':
float(scores[index]),
'label':
label
})
self._data.valid_ds.tfms = valid_tfms
predictions, labels, scores = _get_transformed_predictions(chips)
# Scale the predictions to original image and clip the predictions to image dims
y_ratio = orig_height / height
x_ratio = orig_width / width
for index, prediction in enumerate(predictions):
prediction[0] = prediction[0] * x_ratio
prediction[1] = prediction[1] * y_ratio
prediction[2] = prediction[2] * x_ratio
prediction[3] = prediction[3] * y_ratio
# Clip xmin
if prediction[0] < 0:
prediction[2] = prediction[2] + prediction[0]
prediction[0] = 1
# Clip width when xmax greater than original width
if prediction[0] + prediction[2] > orig_width:
prediction[2] = (prediction[0] + prediction[2]) - orig_width
# Clip ymin
if prediction[1] < 0:
prediction[3] = prediction[3] + prediction[1]
prediction[1] = 1
# Clip height when ymax greater than original height
if prediction[1] + prediction[3] > orig_height:
prediction[3] = (prediction[1] + prediction[3]) - orig_height
predictions[index] = [
prediction[0], prediction[1], prediction[2], prediction[3]
]
if visualize:
image = _draw_predictions(orig_frame,
predictions,
labels,
color=(255, 0, 0),
fontface=2,
thickness=1)
import matplotlib.pyplot as plt
image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)
if getattr(self._data, "_is_coco", "") == True:
figsize = (20, 20)
else:
figsize = (4, 4)
fig, ax = plt.subplots(1, 1, figsize=figsize)
ax.imshow(image)
if return_scores:
return predictions, labels, scores
else:
return predictions, labels
def predict_video(self,
input_video_path,
metadata_file,
threshold=0.5,
nms_overlap=0.1,
track=False,
visualize=False,
output_file_path=None,
multiplex=False,
multiplex_file_path=None,
tracker_options={
'assignment_iou_thrd': 0.3,
'vanish_frames': 40,
'detect_frames': 10
},
visual_options={
'show_scores': True,
'show_labels': True,
'thickness': 2,
'fontface': 0,
'color': (255, 255, 255)
},
resize=False):
"""
Runs prediction on a video and appends the output VMTI predictions in the metadata file.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
input_video_path Required. Path to the video file to make the
predictions on.
--------------------- -------------------------------------------
metadata_file Required. Path to the metadata csv file where
the predictions will be saved in VMTI format.
--------------------- -------------------------------------------
threshold Optional float. The probability above which
a detection will be considered.
--------------------- -------------------------------------------
nms_overlap Optional float. The intersection over union
threshold with other predicted bounding
boxes, above which the box with the highest
score will be considered a true positive.
--------------------- -------------------------------------------
track Optional bool. Set this parameter as True to
enable object tracking.
--------------------- -------------------------------------------
visualize Optional boolean. If True a video is saved
with prediction results.
--------------------- -------------------------------------------
output_file_path Optional path. Path of the final video to be saved.
If not supplied, video will be saved at path input_video_path
appended with _prediction.
--------------------- -------------------------------------------
multiplex Optional boolean. Runs Multiplex using the VMTI detections.
--------------------- -------------------------------------------
multiplex_file_path Optional path. Path of the multiplexed video to be saved.
By default a new file with _multiplex.MOV extension is saved
in the same folder.
--------------------- -------------------------------------------
tracking_options Optional dictionary. Set different parameters for
object tracking. assignment_iou_thrd parameter is used
to assign threshold for assignment of trackers,
vanish_frames is the number of frames the object should
be absent to consider it as vanished, detect_frames
is the number of frames an object should be detected
to track it.
--------------------- -------------------------------------------
visual_options Optional dictionary. Set different parameters for
visualization.
show_scores boolean, to view scores on predictions,
show_labels boolean, to view labels on predictions,
thickness integer, to set the thickness level of box,
fontface integer, fontface value from opencv values,
color tuple (B, G, R), tuple containing values between
0-255.
--------------------- -------------------------------------------
resize Optional boolean. Resizes the video frames to the same size
(chip_size parameter in prepare_data) that the model was trained on,
before detecting objects.
Note that if resize_to parameter was used in prepare_data,
the video frames are resized to that size instead.
By default, this parameter is false and the detections are run
in a sliding window fashion by applying the model on cropped sections
of the frame (of the same size as the model was trained on).
===================== ===========================================
"""
VideoUtils.predict_video(self, input_video_path, metadata_file,
threshold, nms_overlap, track, visualize,
output_file_path, multiplex,
multiplex_file_path, tracker_options,
visual_options, resize)
def average_precision_score(self,
detect_thresh=0.5,
iou_thresh=0.1,
mean=False,
show_progress=True):
"""
Computes average precision on the validation set for each class.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
detect_thresh Optional float. The probabilty above which
a detection will be considered for computing
average precision.
--------------------- -------------------------------------------
iou_thresh Optional float. The intersection over union
threshold with the ground truth labels, above
which a predicted bounding box will be
considered a true positive.
--------------------- -------------------------------------------
mean Optional bool. If False returns class-wise
average precision otherwise returns mean
average precision.
===================== ===========================================
:returns: `dict` if mean is False otherwise `float`
"""
self._check_requisites()
aps = compute_class_AP(self,
self._data.valid_dl,
self._data.c - 1,
show_progress,
detect_thresh=detect_thresh,
iou_thresh=iou_thresh)
if mean:
return statistics.mean(aps)
else:
return dict(zip(self._data.classes[1:], aps))
def _get_emd_params(self):
class_data = {}
_emd_template = {}
_emd_template["Framework"] = "arcgis.learn.models._inferencing"
_emd_template["InferenceFunction"] = "ArcGISObjectDetector.py"
_emd_template["ModelConfiguration"] = "_yolov3_inference"
_emd_template["ModelType"] = "ObjectDetection"
_emd_template["ExtractBands"] = [0, 1, 2]
_emd_template['ModelParameters'] = {}
_emd_template['ModelParameters']['anchors'] = self.config_model[
'ANCHORS']
_emd_template['ModelParameters']['n_bands'] = self.config_model[
'N_BANDS']
_emd_template['Classes'] = []
if self._data is not None:
for i, class_name in enumerate(
self._data.classes[1:]): # 0th index is background
inverse_class_mapping = {
v: k
for k, v in self._data.class_mapping.items()
}
class_data["Value"] = inverse_class_mapping[class_name]
class_data["Name"] = class_name
color = [random.choice(range(256)) for i in range(3)]
class_data["Color"] = color
_emd_template['Classes'].append(class_data.copy())
else:
for k, i in coco_class_mapping().items():
class_data['Value'] = k
class_data['Name'] = i
color = [random.choice(range(256)) for i in range(3)]
class_data["Color"] = color
_emd_template['Classes'].append(class_data.copy())
return _emd_template
@classmethod
def from_model(cls, emd_path, data=None):
"""
Creates a YOLOv3 Object Detector from an Esri Model Definition (EMD) file.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
emd_path Required string. Path to Esri Model Definition
file.
--------------------- -------------------------------------------
data Required fastai Databunch or None. Returned data
object from `prepare_data` function or None for
inferencing.
===================== ===========================================
:returns: `YOLOv3` Object
"""
if not HAS_FASTAI:
_raise_fastai_import_error(import_exception=import_exception)
emd_path = Path(emd_path)
emd = json.load(open(emd_path))
model_file = Path(emd['ModelFile'])
chip_size = emd["ImageWidth"]
if not model_file.is_absolute():
model_file = emd_path.parent / model_file
class_mapping = {i['Value']: i['Name'] for i in emd['Classes']}
resize_to = emd.get('resize_to')
if isinstance(resize_to, list):
resize_to = (resize_to[0], resize_to[1])
data_passed = True
# Create an image databunch for when loading the model using emd (without training data)
if data is None:
data_passed = False
train_tfms = []
val_tfms = []
ds_tfms = (train_tfms, val_tfms)
with warnings.catch_warnings():
warnings.simplefilter("ignore", UserWarning)
sd = ImageList([],
path=emd_path.parent.parent).split_by_idx([])
data = sd.label_const(
0,
label_cls=ObjectDetectionCategoryList,
classes=list(class_mapping.values())).transform(
ds_tfms).databunch().normalize(imagenet_stats)
data.chip_size = chip_size
data.class_mapping = class_mapping
data.classes = ['background'] + list(class_mapping.values())
data = get_multispectral_data_params_from_emd(data, emd)
# Add 1 for background class
data.c += 1
data._is_empty = True
data.emd_path = emd_path
data.emd = emd
data.resize_to = resize_to
ret = cls(data, **emd['ModelParameters'], pretrained_path=model_file)
if not data_passed:
ret.learn.data.single_ds.classes = ret._data.classes
ret.learn.data.single_ds.y.classes = ret._data.classes
return ret
class RetinaNet(ArcGISModel):
"""
Creates a RetinaNet Object Detector with the specified zoom scales
and aspect ratios.
Based on the Fast.ai notebook at https://github.com/fastai/fastai_dev/blob/master/dev_nb/102a_coco.ipynb
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
data Required fastai Databunch. Returned data object from
`prepare_data` function.
--------------------- -------------------------------------------
scales Optional list of float values. Zoom scales of anchor boxes.
--------------------- -------------------------------------------
ratios Optional list of float values. Aspect ratios of anchor
boxes.
--------------------- -------------------------------------------
backbone Optional function. Backbone CNN model to be used for
creating the base of the `RetinaNet`, which
is `resnet50` by default.
Compatible backbones: 'resnet18', 'resnet34', 'resnet50', 'resnet101', 'resnet152'
--------------------- -------------------------------------------
pretrained_path Optional string. Path where pre-trained model is
saved.
===================== ===========================================
:returns: `RetinaNet` Object
"""
def __init__(self, data, scales=None, ratios=None, backbone=None, pretrained_path=None):
# Set default backbone to be 'resnet50'
if backbone is None:
backbone = models.resnet50
super().__init__(data, backbone)
n_bands = len(getattr(self._data, '_extract_bands', [0, 1, 2]))
_backbone = self._backbone
if hasattr(self, '_orig_backbone'):
_backbone = self._orig_backbone
# Check if a backbone provided is compatible, use resnet50 as default
if not self._check_backbone_support(_backbone):
raise Exception (f"Enter only compatible backbones from {', '.join(self.supported_backbones)}")
self.name = "RetinaNet"
self._code = code
self.scales = ifnone(scales, [1,2**(-1/3), 2**(-2/3)])
self.ratios = ifnone(ratios, [1/2,1,2])
self._n_anchors = len(self.scales) * len(self.ratios)
self._data = data
self._chip_size = (data.chip_size,data.chip_size)
# Cut-off the backbone before the penultimate layer
self._encoder = create_body(self._backbone, -2)
# Initialize the model, loss function and the Learner object
self._model = RetinaNetModel(self._encoder, n_classes=data.c-1, final_bias=-4, chip_size=self._chip_size, n_anchors=self._n_anchors, n_bands=n_bands)
self._loss_f = RetinaNetFocalLoss(sizes=self._model.sizes, scales=self.scales, ratios=self.ratios)
self.learn = Learner(data, self._model, loss_func=self._loss_f)
self.learn.split([self._model.encoder[6], self._model.c5top5])
self.learn.freeze()
if pretrained_path is not None:
self.load(str(pretrained_path))
self._arcgis_init_callback() # make first conv weights learnable
def __str__(self):
return self.__repr__()
def __repr__(self):
return '<%s>' % (type(self).__name__)
# Return a list of supported backbones names
@property
def supported_backbones(self):
"""
Supported torchvision backbones for this model.
"""
return RetinaNet._supported_backbones()
@staticmethod
def _supported_backbones():
return [*_resnet_family]
def _get_emd_params(self):
_emd_template = {}
_emd_template["Framework"] = "arcgis.learn.models._inferencing"
_emd_template["InferenceFunction"] = "ArcGISObjectDetector.py"
_emd_template["ModelConfiguration"] = "_RetinaNet_Inference"
_emd_template["ModelType"] = "ObjectDetection"
_emd_template["ExtractBands"] = [0, 1, 2]
_emd_template['ModelParameters'] = {}
_emd_template['ModelParameters']['scales'] = self._loss_f.scales #Scales and Ratios are attributes of RetinaNetFocalLoss object _loss_f
_emd_template['ModelParameters']['ratios'] = self._loss_f.ratios
_emd_template['Classes'] = []
class_data = {}
for i, class_name in enumerate(self._data.classes[1:]): # 0th index is background
inverse_class_mapping = {v: k for k, v in self._data.class_mapping.items()}
class_data["Value"] = inverse_class_mapping[class_name]
class_data["Name"] = class_name
color = [random.choice(range(256)) for i in range(3)]
class_data["Color"] = color
_emd_template['Classes'].append(class_data.copy())
return _emd_template
@property
def _model_metrics(self):
return {'accuracy': self.average_precision_score(show_progress=False)}
@classmethod
def from_model(cls, emd_path, data=None):
"""
Creates a RetinaNet Object Detector from an Esri Model Definition (EMD) file.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
emd_path Required string. Path to Esri Model Definition
file.
--------------------- -------------------------------------------
data Required fastai Databunch or None. Returned data
object from `prepare_data` function or None for
inferencing.
===================== ===========================================
:returns: `RetinaNet` Object
"""
if not HAS_FASTAI:
_raise_fastai_import_error(import_exception=import_exception)
emd_path = Path(emd_path)
emd = json.load(open(emd_path))
model_file = Path(emd['ModelFile'])
chip_size = emd["ImageWidth"]
if not model_file.is_absolute():
model_file = emd_path.parent / model_file
class_mapping = {i['Value'] : i['Name'] for i in emd['Classes']}
resize_to = emd.get('resize_to')
if isinstance(resize_to, list):
resize_to = (resize_to[0], resize_to[1])
data_passed = True
# Create an image databunch for when loading the model using emd (without training data)
if data is None:
data_passed = False
train_tfms = []
val_tfms = []
ds_tfms = (train_tfms, val_tfms)
with warnings.catch_warnings():
warnings.simplefilter("ignore", UserWarning)
sd = ImageList([], path=emd_path.parent.parent).split_by_idx([])
data = sd.label_const(0, label_cls=SSDObjectCategoryList, classes=list(class_mapping.values())).transform(ds_tfms).databunch().normalize(imagenet_stats)
data.chip_size = chip_size
data.class_mapping = class_mapping
data.classes = ['background'] + list(class_mapping.values())
data = get_multispectral_data_params_from_emd(data, emd)
# Add 1 for background class
data.c += 1
data._is_empty = True
data.emd_path = emd_path
data.emd = emd
data.resize_to = resize_to
ret = cls(data, **emd['ModelParameters'], pretrained_path=model_file)
if not data_passed:
ret.learn.data.single_ds.classes = ret._data.classes
ret.learn.data.single_ds.y.classes = ret._data.classes
return ret
def show_results(self, rows=5, thresh=0.5, nms_overlap=0.1):
"""
Displays the results of a trained model on a part of the validation set.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
rows Optional int. Number of rows of results
to be displayed.
--------------------- -------------------------------------------
thresh Optional float. The probabilty above which
a detection will be considered valid.
--------------------- -------------------------------------------
nms_overlap Optional float. The intersection over union
threshold with other predicted bounding
boxes, above which the box with the highest
score will be considered a true positive.
===================== ===========================================
"""
self._check_requisites()
if rows > len(self._data.valid_ds):
rows = len(self._data.valid_ds)
self.learn.show_results(rows=rows, thresh=thresh, nms_overlap=nms_overlap, ssd=self)
def _show_results_multispectral(self, rows=5, thresh=0.3, nms_overlap=0.1, alpha=1, **kwargs):
ax = show_results_multispectral(
self,
nrows=rows,
thresh=thresh,
nms_overlap=nms_overlap,
alpha=alpha,
**kwargs
)
def predict_video(
self,
input_video_path,
metadata_file,
threshold=0.5,
nms_overlap=0.1,
track=False,
visualize=False,
output_file_path=None,
multiplex=False,
multiplex_file_path=None,
tracker_options={
'assignment_iou_thrd': 0.3,
'vanish_frames': 40,
'detect_frames': 10
},
visual_options={
'show_scores': True,
'show_labels': True,
'thickness': 2,
'fontface': 0,
'color': (255, 255, 255)
},
resize=False
):
"""
Runs prediction on a video and appends the output VMTI predictions in the metadata file.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
input_video_path Required. Path to the video file to make the
predictions on.
--------------------- -------------------------------------------
metadata_file Required. Path to the metadata csv file where
the predictions will be saved in VMTI format.
--------------------- -------------------------------------------
threshold Optional float. The probability above which
a detection will be considered.
--------------------- -------------------------------------------
nms_overlap Optional float. The intersection over union
threshold with other predicted bounding
boxes, above which the box with the highest
score will be considered a true positive.
--------------------- -------------------------------------------
track Optional bool. Set this parameter as True to
enable object tracking.
--------------------- -------------------------------------------
visualize Optional boolean. If True a video is saved
with prediction results.
--------------------- -------------------------------------------
output_file_path Optional path. Path of the final video to be saved.
If not supplied, video will be saved at path input_video_path
appended with _prediction.
--------------------- -------------------------------------------
multiplex Optional boolean. Runs Multiplex using the VMTI detections.
--------------------- -------------------------------------------
multiplex_file_path Optional path. Path of the multiplexed video to be saved.
By default a new file with _multiplex.MOV extension is saved
in the same folder.
--------------------- -------------------------------------------
tracking_options Optional dictionary. Set different parameters for
object tracking. assignment_iou_thrd parameter is used
to assign threshold for assignment of trackers,
vanish_frames is the number of frames the object should
be absent to consider it as vanished, detect_frames
is the number of frames an object should be detected
to track it.
--------------------- -------------------------------------------
visual_options Optional dictionary. Set different parameters for
visualization.
show_scores boolean, to view scores on predictions,
show_labels boolean, to view labels on predictions,
thickness integer, to set the thickness level of box,
fontface integer, fontface value from opencv values,
color tuple (B, G, R), tuple containing values between
0-255.
--------------------- -------------------------------------------
resize Optional boolean. Resizes the video frames to the same size
(chip_size parameter in prepare_data) that the model was trained on,
before detecting objects.
Note that if resize_to parameter was used in prepare_data,
the video frames are resized to that size instead.
By default, this parameter is false and the detections are run
in a sliding window fashion by applying the model on cropped sections
of the frame (of the same size as the model was trained on).
===================== ===========================================
"""
VideoUtils.predict_video(
self,
input_video_path,
metadata_file,
threshold,
nms_overlap,
track, visualize,
output_file_path,
multiplex,
multiplex_file_path,
tracker_options,
visual_options,
resize
)
def predict(self, image_path, threshold=0.5, nms_overlap=0.1, return_scores=True, visualize=False, resize=False):
"""
Predicts and displays the results of a trained model on a single image.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
image_path Required. Path to the image file to make the
predictions on.
--------------------- -------------------------------------------
thresh Optional float. The probabilty above which
a detection will be considered valid.
--------------------- -------------------------------------------
nms_overlap Optional float. The intersection over union
threshold with other predicted bounding
boxes, above which the box with the highest
score will be considered a true positive.
--------------------- -------------------------------------------
return_scores Optional boolean.
Will return the probability scores of the
bounding box predictions if True.
--------------------- -------------------------------------------
visualize Optional boolean. Displays the image with
predicted bounding boxes if True.
--------------------- -------------------------------------------
resize Optional boolean. Resizes the image to the same size
(chip_size parameter in prepare_data) that the model was trained on,
before detecting objects.
Note that if resize_to parameter was used in prepare_data,
the image is resized to that size instead.
By default, this parameter is false and the detections are run
in a sliding window fashion by applying the model on cropped sections
of the image (of the same size as the model was trained on).
===================== ===========================================
:returns: 'List' of xmin, ymin, width, height of predicted bounding boxes on the given image
"""
if not HAS_OPENCV:
raise Exception("This function requires opencv 4.0.1.24. Install it using pip install opencv-python==4.0.1.24")
if isinstance(image_path, str):
image = cv2.imread(image_path)
else:
image = image_path
orig_height, orig_width, _ = image.shape
orig_frame = image.copy()
if resize and self._data.resize_to is None\
and self._data.chip_size is not None:
image = cv2.resize(image, (self._data.chip_size, self._data.chip_size))
if self._data.resize_to is not None:
if isinstance(self._data.resize_to, tuple):
image = cv2.resize(image, self._data.resize_to)
else:
image = cv2.resize(image, (self._data.resize_to, self._data.resize_to))
height, width, _ = image.shape
if self._data.chip_size is not None:
chips = _get_image_chips(image, self._data.chip_size)
else:
chips = [{'width': width, 'height': height, 'xmin': 0, 'ymin': 0, 'chip': image, 'predictions': []}]
valid_tfms = self._data.valid_ds.tfms
self._data.valid_ds.tfms = []
include_pad_detections = False
if len(chips) == 1:
include_pad_detections = True
for chip in chips:
frame = Image(pil2tensor(PIL.Image.fromarray(cv2.cvtColor(chip['chip'], cv2.COLOR_BGR2RGB)), dtype=np.float32).div_(255))
bbox = self.learn.predict(frame, thresh=threshold, nms_overlap=nms_overlap, ret_scores=True, ssd=self)[0]
if bbox:
scores = bbox.scores
bboxes, lbls = bbox._compute_boxes()
bboxes.add_(1).mul_(
torch.tensor([chip['height'] / 2, chip['width'] / 2, chip['height'] / 2, chip['width'] / 2])).long()
for index, bbox in enumerate(bboxes):
if lbls is not None:
label = lbls[index]
else:
label = 'Default'
data = bb2hw(bbox)
if include_pad_detections or not _exclude_detection((data[0], data[1], data[2], data[3]), chip['width'], chip['height']):
chip['predictions'].append({
'xmin': data[0],
'ymin': data[1],
'width': data[2],
'height': data[3],
'score': float(scores[index]),
'label': label
})
self._data.valid_ds.tfms = valid_tfms
predictions, labels, scores = _get_transformed_predictions(chips)
# Scale the predictions to original image and clip the predictions to image dims
y_ratio = orig_height/height
x_ratio = orig_width/width
for index, prediction in enumerate(predictions):
prediction[0] = prediction[0]*x_ratio
prediction[1] = prediction[1]*y_ratio
prediction[2] = prediction[2]*x_ratio
prediction[3] = prediction[3]*y_ratio
# Clip xmin
if prediction[0] < 0:
prediction[2] = prediction[2] + prediction[0]
prediction[0] = 1
# Clip width when xmax greater than original width
if prediction[0] + prediction[2] > orig_width:
prediction[2] = (prediction[0] + prediction[2]) - orig_width
# Clip ymin
if prediction[1] < 0:
prediction[3] = prediction[3] + prediction[1]
prediction[1] = 1
# Clip height when ymax greater than original height
if prediction[1] + prediction[3] > orig_height:
prediction[3] = (prediction[1] + prediction[3]) - orig_height
predictions[index] = [
prediction[0],
prediction[1],
prediction[2],
prediction[3]
]
if visualize:
image = _draw_predictions(orig_frame, predictions, labels)
import matplotlib.pyplot as plt
plt.xticks([])
plt.yticks([])
image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)
plt.imshow(PIL.Image.fromarray(image))
if return_scores:
return predictions, labels, scores
else:
return predictions, labels
def average_precision_score(self, detect_thresh=0.5, iou_thresh=0.1, mean=False, show_progress=True):
"""
Computes average precision on the validation set for each class.
===================== ===========================================
**Argument** **Description**
--------------------- -------------------------------------------
detect_thresh Optional float. The probabilty above which
a detection will be considered for computing
average precision.
--------------------- -------------------------------------------
iou_thresh Optional float. The intersection over union
threshold with the ground truth labels, above
which a predicted bounding box will be
considered a true positive.
--------------------- -------------------------------------------
mean Optional bool. If False returns class-wise
average precision otherwise returns mean
average precision.
===================== ===========================================
:returns: `dict` if mean is False otherwise `float`
"""
self._check_requisites()
aps = compute_class_AP(self, self._data.valid_dl, self._data.c - 1, show_progress, detect_thresh=detect_thresh, iou_thresh=iou_thresh)
if mean:
return statistics.mean(aps)
else:
return dict(zip(self._data.classes[1:], aps))
def plot_confusion_matrix_for_patients(data:ImageDataBunch, learn:Learner, normalize:bool=True) -> None:
"""
Plot confusion matrix per patient.
"""
# make inference on `data.valid_ds` and build dictionary: <fname>:(<actual_label>, <predicted_label>)
# which contains predictions per slice
res_dict = dict()
for idx in range(len(data.valid_ds)):
img = data.valid_ds[idx][0]
label_actual = str(data.valid_ds[idx][1])
label_predict, _, _ = learn.predict(img)
label_predict = str(label_predict)
fname = data.valid_dl.dataset.items[idx].stem
res_dict[fname] = label_actual, label_predict
# calculate dictionary with dictionary of prediction counters per patient
nested_patient = dict()
for key in res_dict:
label_predict = res_dict[key][1]
patient_id = key[:-6]
# if there is no patient with such `patient_id` - create it, othervise - create it
if patient_id in nested_patient.keys():
# update current walue, if we have this label for this patient, othervise create it
if label_predict in nested_patient[patient_id]["predictions"].keys():
nested_patient[patient_id]["predictions"][label_predict] += 1
else: # create this label
nested_patient[patient_id]["predictions"][label_predict] = 1
else:
label_actual = res_dict[key][0]
nested_patient[patient_id] = {"predictions": {label_predict : 1}, "actual": label_actual}
# modify `nested_patient` dictionary to left prediction with the maximum counter
for patient_id in nested_patient:
nested_patient[patient_id]["predictions"] = max(nested_patient[patient_id]["predictions"], key=nested_patient[patient_id]["predictions"].get)
# create list with labels: predicted and actual
y_true = []
y_pred = []
for patient_id in nested_patient:
y_true.append(nested_patient[patient_id]["actual"])
y_pred.append(nested_patient[patient_id]["predictions"])
# make plotting
classes = learn.data.classes
# compute confusion matrix(y_true, y_pred)
cm = confusion_matrix(y_true, y_pred)
if normalize:
cm = cm.astype('float') / cm.sum(axis=1)[:, np.newaxis]
fig, ax = plt.subplots()
im = ax.imshow(cm, interpolation='nearest', cmap=plt.cm.Blues)
ax.figure.colorbar(im, ax=ax)
# We want to show all ticks...
ax.set(xticks=np.arange(cm.shape[1]),
yticks=np.arange(cm.shape[0]),
# ... and label them with the respective list entries
xticklabels=classes, yticklabels=classes,
title="Per patient confusion matrix",
ylabel='Actual',
xlabel='Predicted')
ax.set_ylim(len(classes)- .5, -.5)
# Rotate the tick labels and set their alignment.
plt.setp(ax.get_xticklabels(), rotation=45, ha="right",
rotation_mode="anchor")
# Loop over data dimensions and create text annotations.
fmt = '.2f' if normalize else 'd'
thresh = cm.max() / 2.
for i in range(cm.shape[0]):
for j in range(cm.shape[1]):
ax.text(j, i, format(cm[i, j], fmt),
ha="center", va="center",
color="white" if cm[i, j] > thresh else "black")
fig.tight_layout()
