SEG 2020 and other idle fixes

README.md

@@ -158,7 +158,7 @@ wget -o /dev/null -O dataset.h5 https://zenodo.org/record/3924682/files/dataset.
 # convert penobscot
 python byod_penobscot.py --filename dataset.h5 --outdir <where to output data>
 # preprocess for experiments
-python prepare_dutchf3.py split_train_val patch --data_dir=<outdir from the previous step> --label_file=train/train_labels.npy --output_dir=splits --stride=50 --patch_size=100 --split_direction=both --section_stride=100
+python prepare_dutchf3.py split_train_val patch --data_dir=<outdir from the previous step> --label_file=train/train_labels.npy --output_dir=splits --stride=50 --patch_size=100 --split_direction=both
 ```
 
 ### Run Examples
@@ -226,12 +226,20 @@ For seismic interpretation (segmentation), if you want to visualize cross-sectio
 
 To install [segyviewer](https://github.com/equinor/segyviewer) run:
 ```bash
-conda env create -n segyviewer python=2.7
+conda create -n segyviewer python=2.7
 conda activate segyviewer
-conda install -c anaconda pyqt=4.11.4
+sudo apt install libqtwebkit4
+conda install -c conda-forge pyqt=4.11.4
 pip install segyviewer
 ```
 
+If you run into any QtPy4 related problems after the installation, try running:
+```bash
+sudo add-apt-repository ppa:rock-core/qt4
+sudo apt update
+sudo apt install libqt4-designer libqt4-opengl libqt4-svg libqtgui4 libqtwebkit4
+```
+
 To visualize cross-sections of a 3D volume, you can run
 [segyviewer](https://github.com/equinor/segyviewer) like so:
 ```bash

cv_lib/cv_lib/segmentation/lovasz_losses.py

@@ -0,0 +1,258 @@
+# Copyright (c) Microsoft Corporation.
+# Licensed under the MIT License.
+
+"""
+DO NOT REMOVE THIS COMMENT
+Lovasz-Softmax and Jaccard hinge loss in PyTorch
+Maxim Berman 2018 ESAT-PSI KU Leuven (MIT License)
+taken from https://github.com/bermanmaxim/LovaszSoftmax under MIT license
+"""
+
+from __future__ import print_function, division
+
+import torch
+from torch.autograd import Variable
+import torch.nn.functional as F
+import numpy as np
+
+try:
+    from itertools import ifilterfalse
+except ImportError:  # py3k
+    from itertools import filterfalse as ifilterfalse
+
+
+def lovasz_grad(gt_sorted):
+    """
+    Computes gradient of the Lovasz extension w.r.t sorted errors
+    See Alg. 1 in paper
+    """
+    p = len(gt_sorted)
+    gts = gt_sorted.sum()
+    intersection = gts - gt_sorted.float().cumsum(0)
+    union = gts + (1 - gt_sorted).float().cumsum(0)
+    jaccard = 1. - intersection / union
+    if p > 1:  # cover 1-pixel case
+        jaccard[1:p] = jaccard[1:p] - jaccard[0:-1]
+    return jaccard
+
+
+def iou_binary(preds, labels, EMPTY=1., ignore=None, per_image=True):
+    """
+    IoU for foreground class
+    binary: 1 foreground, 0 background
+    """
+    if not per_image:
+        preds, labels = (preds,), (labels,)
+    ious = []
+    for pred, label in zip(preds, labels):
+        intersection = ((label == 1) & (pred == 1)).sum()
+        union = ((label == 1) | ((pred == 1) & (label != ignore))).sum()
+        if not union:
+            iou = EMPTY
+        else:
+            iou = float(intersection) / float(union)
+        ious.append(iou)
+    iou = mean(ious)  # mean accross images if per_image
+    return 100 * iou
+
+
+def iou(preds, labels, C, EMPTY=1., ignore=None, per_image=False):
+    """
+    Array of IoU for each (non ignored) class
+    """
+    if not per_image:
+        preds, labels = (preds,), (labels,)
+    ious = []
+    for pred, label in zip(preds, labels):
+        iou = []
+        for i in range(C):
+            if i != ignore:  # The ignored label is sometimes among predicted classes (ENet - CityScapes)
+                intersection = ((label == i) & (pred == i)).sum()
+                union = ((label == i) | ((pred == i) & (label != ignore))).sum()
+                if not union:
+                    iou.append(EMPTY)
+                else:
+                    iou.append(float(intersection) / float(union))
+        ious.append(iou)
+    ious = [mean(iou) for iou in zip(*ious)]  # mean accross images if per_image
+    return 100 * np.array(ious)
+
+
+# --------------------------- BINARY LOSSES ---------------------------
+
+
+def lovasz_hinge(logits, labels, per_image=True, ignore=None):
+    """
+    Binary Lovasz hinge loss
+      logits: [B, H, W] Variable, logits at each pixel (between -\infty and +\infty)
+      labels: [B, H, W] Tensor, binary ground truth masks (0 or 1)
+      per_image: compute the loss per image instead of per batch
+      ignore: void class id
+    """
+    if per_image:
+        loss = mean(lovasz_hinge_flat(*flatten_binary_scores(log.unsqueeze(0), lab.unsqueeze(0), ignore))
+                    for log, lab in zip(logits, labels))
+    else:
+        loss = lovasz_hinge_flat(*flatten_binary_scores(logits, labels, ignore))
+    return loss
+
+
+def lovasz_hinge_flat(logits, labels):
+    """
+    Binary Lovasz hinge loss
+      logits: [P] Variable, logits at each prediction (between -\infty and +\infty)
+      labels: [P] Tensor, binary ground truth labels (0 or 1)
+      ignore: label to ignore
+    """
+    if len(labels) == 0:
+        # only void pixels, the gradients should be 0
+        return logits.sum() * 0.
+    signs = 2. * labels.float() - 1.
+    errors = (1. - logits * Variable(signs))
+    errors_sorted, perm = torch.sort(errors, dim=0, descending=True)
+    perm = perm.data
+    gt_sorted = labels[perm]
+    grad = lovasz_grad(gt_sorted)
+    loss = torch.dot(F.relu(errors_sorted), Variable(grad))
+    return loss
+
+
+def flatten_binary_scores(scores, labels, ignore=None):
+    """
+    Flattens predictions in the batch (binary case)
+    Remove labels equal to 'ignore'
+    """
+    scores = scores.view(-1)
+    labels = labels.view(-1)
+    if ignore is None:
+        return scores, labels
+    valid = (labels != ignore)
+    vscores = scores[valid]
+    vlabels = labels[valid]
+    return vscores, vlabels
+
+
+class StableBCELoss(torch.nn.modules.Module):
+    def __init__(self):
+        super(StableBCELoss, self).__init__()
+
+    def forward(self, input, target):
+        neg_abs = - input.abs()
+        loss = input.clamp(min=0) - input * target + (1 + neg_abs.exp()).log()
+        return loss.mean()
+
+
+def binary_xloss(logits, labels, ignore=None):
+    """
+    Binary Cross entropy loss
+      logits: [B, H, W] Variable, logits at each pixel (between -\infty and +\infty)
+      labels: [B, H, W] Tensor, binary ground truth masks (0 or 1)
+      ignore: void class id
+    """
+    logits, labels = flatten_binary_scores(logits, labels, ignore)
+    loss = StableBCELoss()(logits, Variable(labels.float()))
+    return loss
+
+
+# --------------------------- MULTICLASS LOSSES ---------------------------
+
+
+def lovasz_softmax(probas, labels, classes='present', per_image=False, ignore=None):
+    """
+    Multi-class Lovasz-Softmax loss
+      probas: [B, C, H, W] Variable, class probabilities at each prediction (between 0 and 1).
+              Interpreted as binary (sigmoid) output with outputs of size [B, H, W].
+      labels: [B, H, W] Tensor, ground truth labels (between 0 and C - 1)
+      classes: 'all' for all, 'present' for classes present in labels, or a list of classes to average.
+      per_image: compute the loss per image instead of per batch
+      ignore: void class labels
+    """
+    if per_image:
+        loss = mean(lovasz_softmax_flat(*flatten_probas(prob.unsqueeze(0), lab.unsqueeze(0), ignore), classes=classes)
+                    for prob, lab in zip(probas, labels))
+    else:
+        loss = lovasz_softmax_flat(*flatten_probas(probas, labels, ignore), classes=classes)
+    return loss
+
+
+def lovasz_softmax_flat(probas, labels, classes='present'):
+    """
+    Multi-class Lovasz-Softmax loss
+      probas: [P, C] Variable, class probabilities at each prediction (between 0 and 1)
+      labels: [P] Tensor, ground truth labels (between 0 and C - 1)
+      classes: 'all' for all, 'present' for classes present in labels, or a list of classes to average.
+    """
+    if probas.numel() == 0:
+        # only void pixels, the gradients should be 0
+        return probas * 0.
+    C = probas.size(1)
+    losses = []
+    class_to_sum = list(range(C)) if classes in ['all', 'present'] else classes
+    for c in class_to_sum:
+        fg = (labels == c).float()  # foreground for class c
+        if (classes is 'present' and fg.sum() == 0):
+            continue
+        if C == 1:
+            if len(classes) > 1:
+                raise ValueError('Sigmoid output possible only with 1 class')
+            class_pred = probas[:, 0]
+        else:
+            class_pred = probas[:, c]
+        errors = (Variable(fg) - class_pred).abs()
+        errors_sorted, perm = torch.sort(errors, 0, descending=True)
+        perm = perm.data
+        fg_sorted = fg[perm]
+        losses.append(torch.dot(errors_sorted, Variable(lovasz_grad(fg_sorted))))
+    return mean(losses)
+
+
+def flatten_probas(probas, labels, ignore=None):
+    """
+    Flattens predictions in the batch
+    """
+    if probas.dim() == 3:
+        # assumes output of a sigmoid layer
+        B, H, W = probas.size()
+        probas = probas.view(B, 1, H, W)
+    B, C, H, W = probas.size()
+    probas = probas.permute(0, 2, 3, 1).contiguous().view(-1, C)  # B * H * W, C = P, C
+    labels = labels.view(-1)
+    if ignore is None:
+        return probas, labels
+    valid = (labels != ignore)
+    vprobas = probas[valid.nonzero().squeeze()]
+    vlabels = labels[valid]
+    return vprobas, vlabels
+
+
+def xloss(logits, labels, ignore=None):
+    """
+    Cross entropy loss
+    """
+    return F.cross_entropy(logits, Variable(labels), ignore_index=255)
+
+
+# --------------------------- HELPER FUNCTIONS ---------------------------
+def isnan(x):
+    return x != x
+
+
+def mean(l, ignore_nan=False, empty=0):
+    """
+    nanmean compatible with generators.
+    """
+    l = iter(l)
+    if ignore_nan:
+        l = ifilterfalse(isnan, l)
+    try:
+        n = 1
+        acc = next(l)
+    except StopIteration:
+        if empty == 'raise':
+            raise ValueError('Empty mean')
+        return empty
+    for n, v in enumerate(l, 2):
+        acc += v
+    if n == 1:
+        return acc
+    return acc / n

cv_lib/cv_lib/segmentation/models/unet.py

@@ -4,6 +4,8 @@
 """ Taken from https://github.com/milesial/Pytorch-UNet
 
 """
+import os
+
 import torch
 import torch.nn as nn
 import torch.nn.functional as F

environment/anaconda/local/environment.yml

@@ -19,6 +19,7 @@ dependencies:
   - papermill>=1.0.1
   - jupyterlab
   - pip:
+    - memory_profiler
     - segyio==1.8.8
     - pytorch-ignite==0.3.0
     - fire==0.2.1

experiments/interpretation/dutchf3_patch/configs/hrnet.yaml

@@ -67,7 +67,7 @@ MODEL:
       FUSE_METHOD: SUM
 
 TRAIN:
-  BATCH_SIZE_PER_GPU: 16
+  BATCH_SIZE_PER_GPU: 32
   BEGIN_EPOCH: 0
   END_EPOCH: 300
   MIN_LR: 0.001

experiments/interpretation/dutchf3_patch/configs/unet.yaml

@@ -11,7 +11,7 @@ WORKERS: 4
 PRINT_FREQ: 10
 LOG_CONFIG: logging.conf
 SEED: 2019
-
+OPENCV_BORDER_CONSTANT: 0
 
 DATASET:
   NUM_CLASSES: 6
@@ -21,7 +21,7 @@ DATASET:
   MAX: 1
 
 MODEL:
-  NAME: resnet_unet
+  NAME: unet
   IN_CHANNELS: 3