Merge pull request #1229 from MouseLand/bfloat16_quantization

Bfloat16 quantization

Author: mrariden

cellpose/core.py

@@ -109,7 +109,7 @@ def assign_device(use_torch=True, gpu=False, device=0):
     return device, gpu
 
 
-def _to_device(x, device):
+def _to_device(x, device, dtype=torch.float32):
     """
     Converts the input tensor or numpy array to the specified device.
 
@@ -121,7 +121,7 @@ def _to_device(x, device):
         torch.Tensor: The converted tensor on the specified device.
     """
     if not isinstance(x, torch.Tensor):
-        X = torch.from_numpy(x).to(device, dtype=torch.float32)
+        X = torch.from_numpy(x).to(device, dtype=dtype)
         return X
     else:
         return x
@@ -137,7 +137,8 @@ def _from_device(X):
     Returns:
         numpy.ndarray: The converted NumPy array.
     """
-    x = X.detach().cpu().numpy()
+    # The cast is so numpy conversion always works
+    x = X.detach().cpu().to(torch.float32).numpy()
     return x
 
 
@@ -151,7 +152,7 @@ def _forward(net, x):
     Returns:
         Tuple[numpy.ndarray, numpy.ndarray]: The output predictions (flows and cellprob) and style features.
     """
-    X = _to_device(x, device=net.device)
+    X = _to_device(x, device=net.device, dtype=net.dtype)
     net.eval()
     with torch.no_grad():
         y, style = net(X)[:2]

cellpose/models.py

@@ -89,7 +89,7 @@ class CellposeModel():
     """
 
     def __init__(self, gpu=False, pretrained_model="cpsam", model_type=None,
-                 diam_mean=None, device=None, nchan=None):
+                 diam_mean=None, device=None, nchan=None, use_bfloat16=True):
         """
         Initialize the CellposeModel.
 
@@ -99,6 +99,7 @@ def __init__(self, gpu=False, pretrained_model="cpsam", model_type=None,
             model_type (str, optional): Any model that is available in the GUI, use name in GUI e.g. "livecell" (can be user-trained or model zoo).
             diam_mean (float, optional): Mean "diameter", 30. is built-in value for "cyto" model; 17. is built-in value for "nuclei" model; if saved in custom model file (cellpose>=2.0) then it will be loaded automatically and overwrite this value.
             device (torch device, optional): Device used for model running / training (torch.device("cuda") or torch.device("cpu")), overrides gpu input, recommended if you want to use a specific GPU (e.g. torch.device("cuda:1")).
+            use_bfloat16 (bool, optional): Use 16bit float precision instead of 32bit for model weights. Default to 16bit (True).
         """
         if diam_mean is not None:
             models_logger.warning(
@@ -139,7 +140,8 @@ def __init__(self, gpu=False, pretrained_model="cpsam", model_type=None,
                 )
 
         self.pretrained_model = pretrained_model
-        self.net = Transformer().to(self.device)
+        dtype = torch.bfloat16 if use_bfloat16 else torch.float32
+        self.net = Transformer(dtype=dtype).to(self.device)
 
         if os.path.exists(self.pretrained_model):
             models_logger.info(f">>>> loading model {self.pretrained_model}")

cellpose/train.py

@@ -48,7 +48,7 @@ def _loss_fn_seg(lbl, y, device):
     veci = 5. * lbl[:, -2:]
     loss = criterion(y[:, -3:-1], veci)
     loss /= 2.
-    loss2 = criterion2(y[:, -1], (lbl[:, -3] > 0.5).float())
+    loss2 = criterion2(y[:, -1], (lbl[:, -3] > 0.5).to(y.dtype))
     loss = loss + loss2
     return loss
 
@@ -454,6 +454,11 @@ def train_seg(net, train_data=None, train_labels=None, train_files=None,
             # network and loss optimization
             X = torch.from_numpy(imgi).to(device)
             lbl = torch.from_numpy(lbl).to(device)
+
+            if X.dtype != net.dtype:
+                X = X.to(net.dtype)
+                lbl = lbl.to(net.dtype)
+
             y = net(X)[0]
             loss = _loss_fn_seg(lbl, y, device)
             if y.shape[1] > 3:

cellpose/vit_sam.py

@@ -10,7 +10,7 @@
 
 class Transformer(nn.Module):
     def __init__(self, backbone="vit_l", ps=8, nout=3, bsize=256, rdrop=0.4,
-                  checkpoint=None):
+                  checkpoint=None, dtype=torch.float32):
         super(Transformer, self).__init__()
 
         # instantiate the vit model, default to not loading SAM
@@ -49,6 +49,8 @@ def __init__(self, backbone="vit_l", ps=8, nout=3, bsize=256, rdrop=0.4,
         for blk in self.encoder.blocks:
             blk.window_size = 0
 
+        self.dtype = dtype
+
     def forward(self, x):      
         # same progression as SAM until readout
         x = self.encoder.patch_embed(x)
@@ -59,7 +61,7 @@ def forward(self, x):
         if self.training and self.rdrop > 0:
             nlay = len(self.encoder.blocks)
             rdrop = (torch.rand((len(x), nlay), device=x.device) < 
-                     torch.linspace(0, self.rdrop, nlay, device=x.device)).float()
+                     torch.linspace(0, self.rdrop, nlay, device=x.device)).to(x.dtype)
             for i, blk in enumerate(self.encoder.blocks):            
                 mask = rdrop[:,i].unsqueeze(-1).unsqueeze(-1).unsqueeze(-1)
                 x = x * mask + blk(x) * (1-mask)
@@ -90,6 +92,9 @@ def load_model(self, PATH, device, strict = False):
         else:
             self.load_state_dict(state_dict, strict = strict)
 
+        if self.dtype != torch.float32:
+            self = self.to(self.dtype)
+
 
     @property
     def device(self):