--- a
+++ b/train_reconstruction.py
@@ -0,0 +1,417 @@
+import torch.nn as nn
+import numpy as np
+import itertools
+import os
+import sys
+
+import torch.optim as optim
+from torch.utils.data import DataLoader
+from torch.autograd import Variable
+from tqdm import tqdm
+import time
+from torch.utils.tensorboard import SummaryWriter
+from pytorch3d.structures import Meshes
+from pytorch3d import loss
+
+from network_reconstruction import *
+from dataio_reconstruction import *
+from utils import *
+
+
+lr = 1e-4
+n_worker = 4
+bs = 5
+n_epoch = 400
+base_err = 10000
+
+w_smooth = 20
+w_surface = 0.5
+w_h = 0.5
+width = 128
+height = 128
+depth = 64
+temper = 3
+
+
+
+model_save_path = './models/model_reconstruction'
+if not os.path.exists(model_save_path):
+    os.makedirs(model_save_path)
+
+# pytorch only saves the last model
+Deform_save_path = os.path.join(model_save_path, 'deform.pth')
+Motion_LA_save_path = os.path.join(model_save_path, 'multiview.pth')
+
+DeformNet = deformnet().cuda()
+MV_LA = Mesh_2d().cuda()
+
+
+optimizer = optim.Adam(filter(lambda p: p.requires_grad,
+                              itertools.chain(DeformNet.parameters(), MV_LA.parameters())), lr=lr)
+Tensor = torch.cuda.FloatTensor
+TensorLong = torch.cuda.LongTensor
+
+# visualisation
+writer = SummaryWriter('./runs/model_reconstruction')
+
+
+
+def train(epoch):
+    DeformNet.train()
+    MV_LA.train()
+
+    epoch_loss = []
+    epoch_seg_loss = []
+    epoch_smooth_loss = []
+    epoch_surface_loss = []
+    epoch_huber_loss = []
+
+
+
+    for batch_idx, batch in tqdm(enumerate(training_data_loader, 1),
+                                 total=len(training_data_loader)):
+
+        img_sa_t, img_sa_ed, img_2ch_t, img_2ch_ed, img_4ch_t, img_4ch_ed, contour_sa_ed, contour_2ch_ed, contour_4ch_ed, \
+        vertex_tpl_ed, faces_tpl, affine_inv, affine, origin, vertex_ed, mesh2seg_sa, mesh2seg_2ch, mesh2seg_4ch = batch
+
+
+        x_sa_ed = Variable(img_sa_ed.type(Tensor))
+        x_2ch_t = Variable(img_2ch_t.type(Tensor))
+        x_2ch_ed = Variable(img_2ch_ed.type(Tensor))
+        x_4ch_t = Variable(img_4ch_t.type(Tensor))
+        x_4ch_ed = Variable(img_4ch_ed.type(Tensor))
+
+
+        aff_sa_inv = Variable(affine_inv[:, 0,:,:].type(Tensor))
+        aff_sa = Variable(affine[:, 0,:,:].type(Tensor))
+        aff_2ch_inv = Variable(affine_inv[:, 1,:,:].type(Tensor))
+        aff_4ch_inv = Variable(affine_inv[:, 2,:,:].type(Tensor))
+
+        origin_sa = Variable(origin[:, 0:1, :].type(Tensor))
+        origin_2ch = Variable(origin[:, 1:2, :].type(Tensor))
+        origin_4ch = Variable(origin[:, 2:3, :].type(Tensor))
+
+        vertex_tpl_0 = Variable(vertex_tpl_ed.permute(0,2,1).type(Tensor)) # [bs, 3, number of vertices]
+        faces_tpl_0 = Variable(faces_tpl.type(Tensor)) # [bs, number of faces, 3]
+        vertex_0 = Variable(vertex_ed.permute(0, 2, 1).type(Tensor))  # [bs, 3, number of vertices]
+
+
+        mesh2seg_sa_gt = Variable(mesh2seg_sa.type(Tensor))
+        mesh2seg_2ch_gt = Variable(mesh2seg_2ch.type(Tensor))
+        mesh2seg_4ch_gt = Variable(mesh2seg_4ch.type(Tensor))
+
+
+
+        optimizer.zero_grad()
+
+        net_la = MV_LA(x_2ch_t, x_2ch_ed, x_4ch_t, x_4ch_ed)
+        net_df = DeformNet(x_sa_ed, net_la['conv2s_2ch'], net_la['conv2s_4ch'])
+
+
+        # ---------------sample from 3D motion fields
+        # translate coordinate
+        v_ed_o = torch.matmul(aff_sa_inv[:, :3, :3], vertex_tpl_0) + aff_sa_inv[:, :3, 3:4]
+        v_ed = v_ed_o.permute(0, 2, 1) - origin_sa  # [bs, number of vertices,3]
+        # normalize translated coordinate (image space) to [-1,1]
+        v_ed_x = (v_ed[:, :, 0:1] - (width / 2)) / (width / 2)
+        v_ed_y = (v_ed[:, :, 1:2] - (height / 2)) / (height / 2)
+        v_ed_z = (v_ed[:, :, 2:3] - (depth / 2)) / (depth / 2)
+        v_ed_norm = torch.cat((v_ed_x, v_ed_y, v_ed_z), 2)
+        v_ed_norm_expand = v_ed_norm.unsqueeze(1).unsqueeze(1)  # [bs, 1, 1,number of vertices,3]
+
+        # sample from 3D motion field
+        pxx = F.grid_sample(net_df['out_def_ed'][:, 0:1], v_ed_norm_expand, align_corners=True).transpose(4, 3)
+        pyy = F.grid_sample(net_df['out_def_ed'][:, 1:2], v_ed_norm_expand, align_corners=True).transpose(4, 3)
+        pzz = F.grid_sample(net_df['out_def_ed'][:, 2:3], v_ed_norm_expand, align_corners=True).transpose(4, 3)
+        # print (pxx.shape, pyy.shape, pzz.shape)
+        delta_p = torch.cat((pxx, pyy, pzz), 4)
+        # updata coor (image space)
+        # print (v_ed.shape, delta_p.shape)
+        v_0_norm_expand = v_ed_norm_expand + delta_p  # [bs, 1, 1,number of vertices,3]
+        # t frame
+        v_0_norm = v_0_norm_expand.squeeze(1).squeeze(1)
+        v_0_x = v_0_norm[:, :, 0:1] * (width / 2) + (width / 2)
+        v_0_y = v_0_norm[:, :, 1:2] * (height / 2) + (height / 2)
+        v_0_z = v_0_norm[:, :, 2:3] * (depth / 2) + (depth / 2)
+        v_0_crop = torch.cat((v_0_x, v_0_y, v_0_z), 2)
+        # translate back to mesh space
+        v_0 = v_0_crop + origin_sa  # [bs, number of vertices,3]
+        pred_v_0 = torch.matmul(aff_sa[:, :3, :3], v_0.permute(0, 2, 1)) + aff_sa[:, :3,3:4]  # [bs, 3, number of vertices]
+        # print (pred_vertex_t.shape)
+
+
+
+        # -------------- differentialable slicer
+
+        # coordinate transformation np.dot(aff_sa_SR_inv[:3,:3], points_ED.T) + aff_sa_SR_inv[:3,3:4]
+        v_sa_hat_ed_o = torch.matmul(aff_sa_inv[:, :3, :3], pred_v_0) + aff_sa_inv[:, :3, 3:4]
+        v_sa_hat_ed = v_sa_hat_ed_o.permute(0, 2, 1) - origin_sa
+        # print (v_sa_hat_t.shape)
+        v_2ch_hat_ed_o = torch.matmul(aff_2ch_inv[:, :3, :3], pred_v_0) + aff_2ch_inv[:, :3, 3:4]
+        v_2ch_hat_ed = v_2ch_hat_ed_o.permute(0, 2, 1) - origin_2ch
+        v_4ch_hat_ed_o = torch.matmul(aff_4ch_inv[:, :3, :3], pred_v_0) + aff_4ch_inv[:, :3, 3:4]
+        v_4ch_hat_ed = v_4ch_hat_ed_o.permute(0,2, 1) - origin_4ch
+
+        # project vertices satisfying threshood
+        # project to SAX slices, project all vertices to a target plane,
+        # vertices selection is moved to loss computation function
+        v_sa_hat_ed_x = torch.clamp(v_sa_hat_ed[:, :, 0:1], min=0, max=height - 1)
+        v_sa_hat_ed_y = torch.clamp(v_sa_hat_ed[:, :, 1:2], min=0, max=width - 1)
+        v_sa_hat_ed_cp = torch.cat((v_sa_hat_ed_x, v_sa_hat_ed_y, v_sa_hat_ed[:, :, 2:3]), 2)
+
+
+        # project to LAX 2CH view
+        v_2ch_hat_ed_x = torch.clamp(v_2ch_hat_ed[:, :, 0:1], min=0, max=height - 1)
+        v_2ch_hat_ed_y = torch.clamp(v_2ch_hat_ed[:, :, 1:2], min=0, max=width - 1)
+        v_2ch_hat_ed_cp = torch.cat((v_2ch_hat_ed_x, v_2ch_hat_ed_y, v_2ch_hat_ed[:, :, 2:3]), 2)
+
+        v_2ch_idx_ed, w_2ch_ed = projection(v_2ch_hat_ed_cp, 0, temper)
+
+
+        # project to LAX 4CH view
+        v_4ch_hat_ed_x = torch.clamp(v_4ch_hat_ed[:, :, 0:1], min=0, max=height - 1)
+        v_4ch_hat_ed_y = torch.clamp(v_4ch_hat_ed[:, :, 1:2], min=0, max=width - 1)
+        v_4ch_hat_ed_cp = torch.cat((v_4ch_hat_ed_x, v_4ch_hat_ed_y, v_4ch_hat_ed[:, :, 2:3]), 2)
+
+        v_4ch_idx_ed, w_4ch_ed = projection(v_4ch_hat_ed_cp, 0, temper)
+
+
+
+        # --------------------- Segmentation loss------------------
+        loss_seg_sa_ed = projection_weightHD_loss_SA(v_sa_hat_ed_cp, temper, height, width, depth, mesh2seg_sa_gt, 'train')
+        loss_seg_2ch_ed = weightedHausdorff_batch(v_2ch_idx_ed, w_2ch_ed, mesh2seg_2ch_gt, height, width, temper, 'train')
+        loss_seg_4ch_ed = weightedHausdorff_batch(v_4ch_idx_ed, w_4ch_ed, mesh2seg_4ch_gt, height, width, temper, 'train')
+
+
+        loss_seg = loss_seg_sa_ed + loss_seg_2ch_ed + loss_seg_4ch_ed
+
+
+        #----------------smoothness loss------------
+        trg_mesh_ed = Meshes(verts=list(pred_v_0.permute(0, 2, 1)), faces=list(faces_tpl_0))
+        loss_laplacian_smooth = loss.mesh_laplacian_smoothing(trg_mesh_ed, method='uniform')
+
+        loss_smooth = loss_laplacian_smooth
+
+        # ------------------J loss---------------------
+        loss_huber = huber_loss_3d(net_df['out_def_ed'])
+
+
+        # ------------------Surface chamfer loss---------------------
+        loss_surface, _ = loss.chamfer_distance(pred_v_0.permute(0, 2, 1), vertex_0.permute(0, 2, 1))
+
+
+        loss_all = loss_seg + w_surface * loss_surface + w_smooth * loss_smooth + w_h * loss_huber
+
+        loss_all.backward()
+        optimizer.step()
+
+
+
+        epoch_loss.append(loss_all.item())
+        epoch_seg_loss.append(loss_seg.item())
+        epoch_smooth_loss.append(loss_smooth.item())
+        epoch_surface_loss.append(loss_surface.item())
+        epoch_huber_loss.append(loss_huber.item())
+
+
+
+        # tensorboard visulisation
+        writer.add_scalar("Loss/train", loss_all, epoch * len(training_data_loader) + batch_idx)
+        writer.add_scalar("Loss/train_seg", loss_seg, epoch * len(training_data_loader) + batch_idx)
+        writer.add_scalar("Loss/train_smooth", loss_smooth, epoch * len(training_data_loader) + batch_idx)
+        writer.add_scalar("Loss/train_huber", loss_huber, epoch * len(training_data_loader) + batch_idx)
+        writer.add_scalar("Loss/train_surface", loss_surface, epoch * len(training_data_loader) + batch_idx)
+
+
+
+        if batch_idx % 40 == 0:
+            print('Train Epoch: {} [{}/{} ({:.0f}%)]\tLoss all: {:.6f}, '
+                  'Seg Loss: {:.6f}, Smooth Loss: {:.6f}, Surface Loss: {:.6f}, Huger Loss: {:.6f},'.format(
+                epoch, batch_idx * len(img_sa_t), len(training_data_loader.dataset),
+                100. * batch_idx / len(training_data_loader), np.mean(epoch_loss),
+                np.mean(epoch_seg_loss), np.mean(epoch_smooth_loss), np.mean(epoch_surface_loss), np.mean(epoch_huber_loss)))
+
+
+def val(epoch):
+    DeformNet.eval()
+    MV_LA.eval()
+
+    val_loss = []
+    val_seg_loss = []
+    val_smooth_loss = []
+    val_surface_loss = []
+    val_huber_loss = []
+
+
+    global base_err
+    for batch_idx, batch in tqdm(enumerate(val_data_loader, 1),
+                                 total=len(val_data_loader)):
+
+        img_sa_t, img_sa_ed, img_2ch_t, img_2ch_ed, img_4ch_t, img_4ch_ed, contour_sa_ed, contour_2ch_ed, contour_4ch_ed, \
+        vertex_tpl_ed, faces_tpl, affine_inv, affine, origin, vertex_ed, mesh2seg_sa, mesh2seg_2ch, mesh2seg_4ch = batch
+
+        with torch.no_grad():
+
+            x_sa_ed = img_sa_ed.type(Tensor)
+            x_2ch_t = img_2ch_t.type(Tensor)
+            x_2ch_ed = img_2ch_ed.type(Tensor)
+            x_4ch_t = img_4ch_t.type(Tensor)
+            x_4ch_ed = img_4ch_ed.type(Tensor)
+
+
+            aff_sa_inv = affine_inv[:, 0, :, :].type(Tensor)
+            aff_sa = affine[:, 0, :, :].type(Tensor)
+            aff_2ch_inv = affine_inv[:, 1, :, :].type(Tensor)
+            aff_4ch_inv = affine_inv[:, 2, :, :].type(Tensor)
+
+
+            origin_sa = origin[:, 0:1, :].type(Tensor)
+            origin_2ch = origin[:, 1:2, :].type(Tensor)
+            origin_4ch = origin[:, 2:3, :].type(Tensor)
+
+            vertex_tpl_0 = vertex_tpl_ed.permute(0, 2, 1).type(Tensor)  # [bs, 3, number of vertices]
+            faces_tpl_0 = faces_tpl.type(Tensor)  # [bs, number of faces, 3]
+            vertex_0 = vertex_ed.permute(0, 2, 1).cuda()  # [bs, 3, number of vertices]
+
+            mesh2seg_sa_gt = Variable(mesh2seg_sa.type(Tensor))
+            mesh2seg_2ch_gt = Variable(mesh2seg_2ch.type(Tensor))
+            mesh2seg_4ch_gt = Variable(mesh2seg_4ch.type(Tensor))
+
+
+            net_la = MV_LA(x_2ch_t, x_2ch_ed, x_4ch_t, x_4ch_ed)
+            net_df = DeformNet(x_sa_ed, net_la['conv2s_2ch'], net_la['conv2s_4ch'])
+
+            # ---------------sample from 3D motion fields
+            # translate coordinate
+            v_ed_o = torch.matmul(aff_sa_inv[:, :3, :3], vertex_tpl_0) + aff_sa_inv[:, :3, 3:4]
+            v_ed = v_ed_o.permute(0, 2, 1) - origin_sa  # [bs, number of vertices,3]
+            # normalize translated coordinate (image space) to [-1,1]
+            v_ed_x = (v_ed[:, :, 0:1] - (width / 2)) / (width / 2)
+            v_ed_y = (v_ed[:, :, 1:2] - (height / 2)) / (height / 2)
+            v_ed_z = (v_ed[:, :, 2:3] - (depth / 2)) / (depth / 2)
+            v_ed_norm = torch.cat((v_ed_x, v_ed_y, v_ed_z), 2)
+            v_ed_norm_expand = v_ed_norm.unsqueeze(1).unsqueeze(1)  # [bs, 1, 1,number of vertices,3]
+
+            # sample from 3D motion field
+            pxx = F.grid_sample(net_df['out_def_ed'][:, 0:1], v_ed_norm_expand, align_corners=True).transpose(4, 3)
+            pyy = F.grid_sample(net_df['out_def_ed'][:, 1:2], v_ed_norm_expand, align_corners=True).transpose(4, 3)
+            pzz = F.grid_sample(net_df['out_def_ed'][:, 2:3], v_ed_norm_expand, align_corners=True).transpose(4, 3)
+            delta_p = torch.cat((pxx, pyy, pzz), 4)
+            # updata coor (image space)
+            # print (v_ed.shape, delta_p.shape)
+            v_0_norm_expand = v_ed_norm_expand + delta_p  # [bs, 1, 1,number of vertices,3]
+            # t frame
+            v_0_norm = v_0_norm_expand.squeeze(1).squeeze(1)
+            v_0_x = v_0_norm[:, :, 0:1] * (width / 2) + (width / 2)
+            v_0_y = v_0_norm[:, :, 1:2] * (height / 2) + (height / 2)
+            v_0_z = v_0_norm[:, :, 2:3] * (depth / 2) + (depth / 2)
+            v_0_crop = torch.cat((v_0_x, v_0_y, v_0_z), 2)
+            # translate back to mesh space
+            v_0 = v_0_crop + origin_sa  # [bs, number of vertices,3]
+            pred_v_0 = torch.matmul(aff_sa[:, :3, :3], v_0.permute(0, 2, 1)) + aff_sa[:, :3,
+                                                                               3:4]  # [bs, 3, number of vertices]
+
+            # -------------- differentialable slicer
+
+            # coordinate transformation np.dot(aff_sa_SR_inv[:3,:3], points_ED.T) + aff_sa_SR_inv[:3,3:4]
+            v_sa_hat_ed_o = torch.matmul(aff_sa_inv[:, :3, :3], pred_v_0) + aff_sa_inv[:, :3, 3:4]
+            v_sa_hat_ed = v_sa_hat_ed_o.permute(0, 2, 1) - origin_sa
+            # print (v_sa_hat_t.shape)
+            v_2ch_hat_ed_o = torch.matmul(aff_2ch_inv[:, :3, :3], pred_v_0) + aff_2ch_inv[:, :3, 3:4]
+            v_2ch_hat_ed = v_2ch_hat_ed_o.permute(0, 2, 1) - origin_2ch
+            v_4ch_hat_ed_o = torch.matmul(aff_4ch_inv[:, :3, :3], pred_v_0) + aff_4ch_inv[:, :3, 3:4]
+            v_4ch_hat_ed = v_4ch_hat_ed_o.permute(0, 2, 1) - origin_4ch
+
+            # project vertices satisfying threshood
+            # project to SAX slices, project all vertices to a target plane,
+            # vertices selection is moved to loss computation function
+            v_sa_hat_ed_x = torch.clamp(v_sa_hat_ed[:, :, 0:1], min=0, max=height - 1)
+            v_sa_hat_ed_y = torch.clamp(v_sa_hat_ed[:, :, 1:2], min=0, max=width - 1)
+            v_sa_hat_ed_cp = torch.cat((v_sa_hat_ed_x, v_sa_hat_ed_y, v_sa_hat_ed[:, :, 2:3]), 2)
+
+
+            # project to LAX 2CH view
+            v_2ch_hat_ed_x = torch.clamp(v_2ch_hat_ed[:, :, 0:1], min=0, max=height - 1)
+            v_2ch_hat_ed_y = torch.clamp(v_2ch_hat_ed[:, :, 1:2], min=0, max=width - 1)
+            v_2ch_hat_ed_cp = torch.cat((v_2ch_hat_ed_x, v_2ch_hat_ed_y, v_2ch_hat_ed[:, :, 2:3]), 2)
+
+            v_2ch_idx_ed, w_2ch_ed = projection(v_2ch_hat_ed_cp, 0, temper)
+
+            # project to LAX 4CH view
+            v_4ch_hat_ed_x = torch.clamp(v_4ch_hat_ed[:, :, 0:1], min=0, max=height - 1)
+            v_4ch_hat_ed_y = torch.clamp(v_4ch_hat_ed[:, :, 1:2], min=0, max=width - 1)
+            v_4ch_hat_ed_cp = torch.cat((v_4ch_hat_ed_x, v_4ch_hat_ed_y, v_4ch_hat_ed[:, :, 2:3]), 2)
+
+            v_4ch_idx_ed, w_4ch_ed = projection(v_4ch_hat_ed_cp, 0, temper)
+
+            # --------------------- Segmentation loss------------------
+            loss_seg_sa_ed = projection_weightHD_loss_SA(v_sa_hat_ed_cp, temper, height, width, depth, mesh2seg_sa_gt,
+                                                         'val')
+
+            loss_seg_2ch_ed = weightedHausdorff_batch(v_2ch_idx_ed, w_2ch_ed, mesh2seg_2ch_gt, height, width, temper,
+                                                      'val')
+            loss_seg_4ch_ed = weightedHausdorff_batch(v_4ch_idx_ed, w_4ch_ed, mesh2seg_4ch_gt, height, width, temper,
+                                                      'val')
+
+            loss_seg = loss_seg_sa_ed + loss_seg_2ch_ed + loss_seg_4ch_ed
+
+            # ----------------smoothness loss------------
+            # print (pred_vertex_t.permute(0,2,1).shape)
+            trg_mesh_ed = Meshes(verts=list(pred_v_0.permute(0, 2, 1)), faces=list(faces_tpl_0))
+            loss_laplacian_smooth = loss.mesh_laplacian_smoothing(trg_mesh_ed, method='uniform')
+
+            loss_smooth = loss_laplacian_smooth
+
+            # ------------------J loss---------------------
+            loss_huber = huber_loss_3d(net_df['out_def_ed'])
+
+
+            # ------------------Surface chamfer loss---------------------
+            loss_surface, _ = loss.chamfer_distance(pred_v_0.permute(0, 2, 1), vertex_0.permute(0, 2, 1))
+
+            loss_all = loss_seg + w_surface * loss_surface + w_smooth * loss_smooth + w_h * loss_huber
+
+
+            val_loss.append(loss_all.item())
+            val_seg_loss.append(loss_seg.item())
+            val_smooth_loss.append(loss_smooth.item())
+            val_surface_loss.append(loss_surface.item())
+            val_huber_loss.append(loss_huber.item())
+
+            if batch_idx == 1:
+                # tensorboard visulisation
+                writer.add_scalar("Loss/val", loss_all, epoch * len(training_data_loader) + batch_idx)
+                writer.add_scalar("Loss/val_seg", loss_seg, epoch * len(training_data_loader) + batch_idx)
+                writer.add_scalar("Loss/val_smooth", loss_smooth, epoch * len(training_data_loader) + batch_idx)
+                writer.add_scalar("Loss/val_huber", loss_huber, epoch * len(training_data_loader) + batch_idx)
+                writer.add_scalar("Loss/val_surface", loss_surface, epoch * len(training_data_loader) + batch_idx)
+
+
+    if np.mean(val_loss) < base_err:
+        torch.save(DeformNet.state_dict(), Deform_save_path)
+        torch.save(MV_LA.state_dict(), Motion_LA_save_path)
+        base_err = np.mean(val_loss)
+
+
+
+data_path = '/train_data_path'
+train_set = TrainDataset(data_path)
+# loading the data
+training_data_loader = DataLoader(dataset=train_set, num_workers=n_worker, batch_size=bs, shuffle=True)
+
+val_data_path = '/val_data_path'
+val_set = ValDataset(val_data_path)
+val_data_loader = DataLoader(dataset=val_set, num_workers=n_worker, batch_size=bs, shuffle=False)
+
+
+for epoch in range(0, n_epoch + 1):
+    start = time.time()
+    train(epoch)
+    end = time.time()
+    print("training took {:.8f}".format(end-start))
+
+    print('Epoch {}'.format(epoch))
+    start = time.time()
+    val(epoch)
+    end = time.time()
+    print("validation took {:.8f}".format(end - start))