Merge pull request #1454 from MouseLand/dino

adding dino models and gpu-accelerated augmentations

Author: carsen-stringer

.github/workflows/test_and_deploy.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: true
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4

cellpose/cli.py

@@ -65,9 +65,9 @@ def get_arg_parser():
 
     # model settings
     model_args = parser.add_argument_group("Model Arguments")
-    model_args.add_argument("--pretrained_model", required=False, default="cpsam",
+    model_args.add_argument("--pretrained_model", required=False, default="cpdino",
                             type=str,
-                            help="model to use for running or starting training")
+                            help="path to model for segmentation or starting training, or builtin model name: cpdino, cpsam_v2, cpdino-vitb, or cpsam")
     model_args.add_argument(
         "--add_model", required=False, default=None, type=str,
         help="model path to copy model to hidden .cellpose folder for using in GUI/CLI")

cellpose/core.py

@@ -292,10 +292,8 @@ def run_3D(net, imgs, batch_size=8, augment=False,
         # per image
         core_logger.info("running %s: %d planes of size (%d, %d)" %
                          (sstr[p], shape[pm[p][0]], shape[pm[p][1]], shape[pm[p][2]]))
-        y, style = run_net(net,
-                           xsl, batch_size=batch_size, augment=augment, 
-                           bsize=bsize, tile_overlap=tile_overlap, 
-                           rsz=None)
+        y, style = run_net(net, xsl, batch_size=batch_size, augment=augment, 
+                           bsize=bsize, tile_overlap=tile_overlap, rsz=None)
         yf[..., -1] += y[..., -1].transpose(ipm[p])
         for j in range(2):
             yf[..., cp[p][j]] += y[..., cpy[p][j]].transpose(ipm[p])

cellpose/denoise.py

@@ -51,7 +51,7 @@
 from cellpose.io import imread
 from cellpose.utils import download_url_to_file
 from cellpose.transforms import pad_image_ND, normalize_img, convert_image
-from cellpose.vit_sam import CPnetBioImageIO
+from cellpose.vit import CPnetBioImageIO
 
 from bioimageio.spec.model.v0_5 import (
     ArchitectureFromFileDescr,

cellpose/export.py

@@ -290,7 +290,7 @@ def __init__(self, image=None, logger=None):
             "learning_rate": 1e-5,
             "weight_decay": 0.1,
             "n_epochs": 100,
-            "model_name": "cpsam" + d.strftime("_%Y%m%d_%H%M%S"),
+            "model_name": "cp4" + d.strftime("_%Y%m%d_%H%M%S"),
         }
 
         self.stitch_threshold = 0.
@@ -496,21 +496,32 @@ def make_buttons(self):
         )
         self.useGPU.setFont(self.medfont)
         self.check_gpu()
-        self.segBoxG.addWidget(self.useGPU, widget_row, 0, 1, 3)
-
-        # compute segmentation with general models
-        self.net_text = ["run CPSAM"]
-        nett = ["cellpose super-generalist model"]
-
-        self.StyleButtons = []
-        jj = 4
-        for j in range(len(self.net_text)):
-            self.StyleButtons.append(
-                guiparts.ModelButton(self, self.net_text[j], self.net_text[j]))
-            w = 5
-            self.segBoxG.addWidget(self.StyleButtons[-1], widget_row, jj, 1, w)
-            jj += w
-            self.StyleButtons[-1].setToolTip(nett[j])
+        self.segBoxG.addWidget(self.useGPU, widget_row, 0, 1, 3)    
+
+        self.progress = QProgressBar(self)
+        self.segBoxG.addWidget(self.progress, widget_row, 3, 1, 5)    
+
+        # compute segmentation with built-in models
+        widget_row += 1
+        self.ModelChooseB = QComboBox()
+        self.ModelChooseB.setFont(self.medfont)
+        current_index = 0
+        self.ModelChooseB.addItems(models.MODEL_NAMES)
+        self.ModelChooseB.setFixedWidth(175)
+        self.ModelChooseB.setCurrentIndex(current_index)
+        tipstr = 'built-in models'
+        self.ModelChooseB.setToolTip(tipstr)
+        self.ModelChooseB.activated.connect(lambda: self.model_choose(custom=False))
+        self.segBoxG.addWidget(self.ModelChooseB, widget_row, 0, 1, 8)
+        
+        # compute segmentation w/ custom model
+        self.ModelButtonB = QPushButton(u"run")
+        self.ModelButtonB.setFont(self.medfont)
+        self.ModelButtonB.setFixedWidth(35)
+        self.ModelButtonB.clicked.connect(
+            lambda: self.compute_segmentation(custom=False))
+        self.segBoxG.addWidget(self.ModelButtonB, widget_row, 8, 1, 1)
+        self.ModelButtonB.setEnabled(False)       
 
         widget_row += 1
         self.ncells = guiparts.ObservableVariable(0)
@@ -521,10 +532,7 @@ def make_buttons(self):
             lambda n: self.roi_count.setText(f'{str(n)} ROIs')
         )
 
-        self.segBoxG.addWidget(self.roi_count, widget_row, 0, 1, 4)
-
-        self.progress = QProgressBar(self)
-        self.segBoxG.addWidget(self.progress, widget_row, 4, 1, 5)
+        self.segBoxG.addWidget(self.roi_count, widget_row, 3, 1, 4)
 
         widget_row += 1
 
@@ -786,15 +794,13 @@ def check_gpu(self, torch=True):
 
 
     def model_choose(self, custom=False):
-        index = self.ModelChooseC.currentIndex(
-        ) if custom else self.ModelChooseB.currentIndex()
-        if index > 0:
-            if custom:
-                model_name = self.ModelChooseC.currentText()
-            else:
-                model_name = self.net_names[index - 1]
-            print(f"GUI_INFO: selected model {model_name}, loading now")
-            self.initialize_model(model_name=model_name, custom=custom)
+        if custom:
+            model_name = self.ModelChooseC.currentText()
+        else:
+            model_name = self.ModelChooseB.currentText()
+        print(f"GUI_INFO: selected model {model_name}")
+        # avoid double-loading model unless we need to?
+        # self.initialize_model(model_name=model_name, custom=custom)
 
     def toggle_scale(self):
         if self.scale_on:
@@ -805,11 +811,10 @@ def toggle_scale(self):
             self.scale_on = True
 
     def enable_buttons(self):
+        self.ModelButtonB.setEnabled(True)
         if len(self.model_strings) > 0:
             self.ModelButtonC.setEnabled(True)
-        for i in range(len(self.StyleButtons)):
-            self.StyleButtons[i].setEnabled(True)
-
+        
         for i in range(len(self.FilterButtons)):
             self.FilterButtons[i].setEnabled(True)
         if self.load_3D:
@@ -1889,8 +1894,8 @@ def get_model_path(self, custom=False):
             self.current_model_path = os.fspath(
                 models.MODEL_DIR.joinpath(self.current_model))
         else:
-            self.current_model = "cpsam"
-            self.current_model_path = models.model_path(self.current_model)
+            self.current_model = self.ModelChooseB.currentText()
+            self.current_model_path = models.cache_model_path(self.current_model)
 
     def initialize_model(self, model_name=None, custom=False):
         if model_name is None or custom:
@@ -1907,7 +1912,7 @@ def initialize_model(self, model_name=None, custom=False):
                 models.MODEL_DIR.joinpath(self.current_model))
 
             self.model = models.CellposeModel(gpu=self.useGPU.isChecked(),
-                                             pretrained_model=self.current_model)
+                                             pretrained_model=self.current_model_path)
 
     def add_model(self):
         io._add_model(self)
@@ -1926,7 +1931,8 @@ def new_model(self):
         image_names = self.get_files()[0]
         self.train_data, self.train_labels, self.train_files, restore, normalize_params = io._get_train_set(
             image_names)
-        TW = guiparts.TrainWindow(self, models.MODEL_NAMES)
+        self.training_params["model_index"] = self.ModelChooseB.currentIndex()
+        TW = guiparts.TrainWindow(self)
         train = TW.exec_()
         if train:
             self.logger.info(
@@ -1944,7 +1950,7 @@ def train_model(self, restore=None, normalize_params=None):
         self.current_model = model_type
 
         self.model = models.CellposeModel(gpu=self.useGPU.isChecked(),
-                                          model_type=model_type)
+                                          pretrained_model=model_type)
         save_path = os.path.dirname(self.filename)
 
         print("GUI_INFO: name of new model: " + self.training_params["model_name"])
@@ -2048,9 +2054,7 @@ def compute_segmentation(self, custom=False, model_name=None, load_model=True):
             print(normalize_params)
             try:
                 masks, flows = self.model.eval(
-                    data, 
-                    diameter=diameter,
-                    cellprob_threshold=cellprob_threshold,
+                    data, diameter=diameter, cellprob_threshold=cellprob_threshold,
                     flow_threshold=flow_threshold, do_3D=do_3D, niter=niter,
                     normalize=normalize_params, stitch_threshold=stitch_threshold,
                     anisotropy=anisotropy, flow3D_smooth=flow3D_smooth,

cellpose/gui/gui.py

@@ -10,6 +10,7 @@
 import numpy as np
 import pathlib, os
 
+from cellpose import models
 from cellpose.gui.io import _save_sets
 
 
@@ -111,32 +112,6 @@ def setup(self):
         )
 
 
-# def create_channel_choose():
-#     # choose channel
-#     ChannelChoose = [QComboBox(), QComboBox()]
-#     ChannelLabels = []
-#     ChannelChoose[0].addItems(["gray", "red", "green", "blue"])
-#     ChannelChoose[1].addItems(["none", "red", "green", "blue"])
-#     cstr = ["chan to segment:", "chan2 (optional): "]
-#     for i in range(2):
-#         ChannelLabels.append(QLabel(cstr[i]))
-#         if i == 0:
-#             ChannelLabels[i].setToolTip(
-#                 "this is the channel in which the cytoplasm or nuclei exist \
-#             that you want to segment")
-#             ChannelChoose[i].setToolTip(
-#                 "this is the channel in which the cytoplasm or nuclei exist \
-#             that you want to segment")
-#         else:
-#             ChannelLabels[i].setToolTip(
-#                 "if <em>cytoplasm</em> model is chosen, and you also have a \
-#             nuclear channel, then choose the nuclear channel for this option")
-#             ChannelChoose[i].setToolTip(
-#                 "if <em>cytoplasm</em> model is chosen, and you also have a \
-#             nuclear channel, then choose the nuclear channel for this option")
-
-#     return ChannelChoose, ChannelLabels
-
 def unsilence_exceptions(func):
     """ Wrapper to unsilence Qt exceptions and re-raise them """
     def wrapper(*args, **kwargs):
@@ -148,19 +123,6 @@ def wrapper(*args, **kwargs):
             logger.debug(''.join(traceback.format_exception(type(e), e, e.__traceback__)))
     return wrapper
 
-class ModelButton(QPushButton):
-
-    def __init__(self, parent, model_name, text):
-        super().__init__()
-        self.setEnabled(False)
-        self.setText(text)
-        self.setFont(parent.boldfont)
-        self.clicked.connect(lambda: self.press(parent))
-        self.model_name = "cpsam"
-
-    def press(self, parent):
-        parent.compute_segmentation(model_name="cpsam")
-
 
 class FilterButton(QPushButton):
 
@@ -428,7 +390,7 @@ def niter(self):
 
 class TrainWindow(QDialog):
 
-    def __init__(self, parent, model_strings):
+    def __init__(self, parent):
         super().__init__(parent)
         self.setGeometry(100, 100, 900, 550)
         self.setWindowTitle("train settings")
@@ -446,7 +408,7 @@ def __init__(self, parent, model_strings):
         # choose initial model
         yoff += 1
         self.ModelChoose = QComboBox()
-        self.ModelChoose.addItems(model_strings)
+        self.ModelChoose.addItems(models.MODEL_NAMES)
         self.ModelChoose.setFixedWidth(150)
         self.ModelChoose.setCurrentIndex(parent.training_params["model_index"])
         self.l0.addWidget(self.ModelChoose, yoff, 1, 1, 1)