Merge branch 'main' of https://github.com/mouseland/cellpose into main

Author: carsen-stringer

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error 
+
+**Run log**
+Please post all command line/notebook output for us to understand the problem. For this please make sure you are running with verbose mode on. So command line, with `--verbose` tag, or in a notebook first run 
+```from cellpose import io 
+logger = io.logger_setup()
+``` 
+before running any Cellpose functions.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[FEATURE]"
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/installation-issue.md

@@ -0,0 +1,23 @@
+---
+name: Installation issue
+about: problems installing cellpose with or without GPU support
+title: "[INSTALL]"
+labels: install
+assignees: ''
+
+---
+
+**Install problem**
+Let us know what issues you are having with installation.
+
+**Environment info**
+Please run `conda list` in your cellpose environment in the terminal / anaconda prompt to let us know your software versions.
+
+**Run log**
+Please post all command line/notebook output for us to understand the problem. For this please make sure you are running with verbose mode on. So command line, with `--verbose` tag, or in a notebook first run 
+
+```from cellpose import io 
+logger = io.logger_setup()
+```
+
+before running any Cellpose functions.

cellpose/__init__.py

@@ -3,4 +3,4 @@
 Welcome to CellposeSAM, cellpose v4.0.1! The neural network component of
 CPSAM is much larger than in previous versions and CPU excution is slow. 
 We encourage users to use GPU/MPS if available. \n\n''' 
-print(message)
+print(message)

cellpose/core.py

@@ -218,7 +218,7 @@ def run_net(net, imgi, batch_size=8, augment=False, tile_overlap=0.1, bsize=224,
             # pad image for net so Ly and Lx are divisible by 4
             imgb = transforms.resize_image(imgi[b], rsz=rsz) if rsz is not None else imgi[b].copy()
             imgb = np.pad(imgb.transpose(2,0,1), pads, mode="constant")
-            IMG, ysub, xsub, Ly, Lx = transforms.make_tiles(
+            IMG, ysub, xsub, Lyt, Lxt = transforms.make_tiles(
                 imgb, bsize=bsize, augment=augment,
                 tile_overlap=tile_overlap)
             IMGa[i * ntiles : (i+1) * ntiles] = np.reshape(IMG, 
@@ -245,7 +245,7 @@ def run_net(net, imgi, batch_size=8, augment=False, tile_overlap=0.1, bsize=224,
                 y = np.reshape(y, (ny, nx, 3, ly, lx))
                 y = transforms.unaugment_tiles(y)
                 y = np.reshape(y, (-1, 3, ly, lx))
-            yfi = transforms.average_tiles(y, ysub, xsub, Ly, Lx)
+            yfi = transforms.average_tiles(y, ysub, xsub, Lyt, Lxt)
             yf[b] = yfi[:, :imgb.shape[-2], :imgb.shape[-1]]
             stylei = stylea[i * ntiles:(i + 1) * ntiles].sum(axis=0)
             stylei /= (stylei**2).sum()**0.5

cellpose/dynamics.py

@@ -486,7 +486,6 @@ def max_pool_nd(h, kernel_size=5):
         del hmax2 
         return hmax
 
-
 def get_masks_torch(pt, inds, shape0, rpad=20, max_size_fraction=0.4):
     """Create masks using pixel convergence after running dynamics.
 
@@ -690,4 +689,4 @@ def compute_masks(dP, cellprob, p=None, niter=200, cellprob_threshold=0.0,
         dynamics_logger.warning(
             "more than 65535 masks in image, masks returned as np.uint32")
 
-    return mask
+    return mask

cellpose/gui/gui.py

@@ -16,7 +16,7 @@
 import cv2
 
 from . import guiparts, menus, io
-from .. import models, core, dynamics, version, denoise, train
+from .. import models, core, dynamics, version, train
 from ..utils import download_url_to_file, masks_to_outlines, diameters
 from ..io import get_image_files, imsave, imread
 from ..transforms import resize_image, normalize99, normalize99_tile, smooth_sharpen_img
@@ -29,14 +29,6 @@
 except:
     MATPLOTLIB = False
 
-try:
-    from google.cloud import storage
-    os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = os.path.join(
-        os.path.dirname(os.path.realpath(__file__)), "key/cellpose-data-writer.json")
-    SERVER_UPLOAD = True
-except:
-    SERVER_UPLOAD = False
-
 Horizontal = QtCore.Qt.Orientation.Horizontal
 
 
@@ -174,7 +166,6 @@ def run(image=None):
     app.setWindowIcon(app_icon)
     app.setStyle("Fusion")
     app.setPalette(guiparts.DarkPalette())
-
     MainW(image=image, logger=logger)
     ret = app.exec_()
     sys.exit(ret)
@@ -187,7 +178,7 @@ def __init__(self, image=None, logger=None):
 
         self.logger = logger
         pg.setConfigOptions(imageAxisOrder="row-major")
-        self.setGeometry(50, 50, 2000, 1500)
+        self.setGeometry(50, 50, 1200, 1000)
         self.setWindowTitle(f"cellpose v{version}")
         self.cp_path = os.path.dirname(os.path.realpath(__file__))
         app_icon = QtGui.QIcon()
@@ -764,7 +755,6 @@ def model_choose(self, custom=False):
             print(f"GUI_INFO: selected model {model_name}, loading now")
             self.initialize_model(model_name=model_name, custom=custom)
 
-
     def toggle_scale(self):
         if self.scale_on:
             self.p0.removeItem(self.scale)
@@ -1604,7 +1594,6 @@ def draw_layer(self):
                 self.outcolor).astype(np.uint8)
 
 
-
     def set_normalize_params(self, normalize_params):
         from cellpose.models import normalize_default
         if self.restore != "filter":
@@ -1760,13 +1749,10 @@ def get_model_path(self, custom=False):
             self.current_model_path = os.fspath(
                 models.MODEL_DIR.joinpath(self.current_model))
         else:
-            self.current_model = self.net_names[max(
-                0,
-                self.ModelChooseB.currentIndex() - 1)]
+            self.current_model = "cpsam"
             self.current_model_path = models.model_path(self.current_model)
 
     def initialize_model(self, model_name=None, custom=False):
-        print(model_name, custom)
         if model_name is None or custom:
             self.get_model_path(custom=custom)
             if not os.path.exists(self.current_model_path):

cellpose/gui/guiparts.py

@@ -143,10 +143,10 @@ def __init__(self, parent, model_name, text):
         self.setText(text)
         self.setFont(parent.boldfont)
         self.clicked.connect(lambda: self.press(parent))
-        self.model_name = model_name if "cyto3" not in model_name else "cyto3"
+        self.model_name = "cpsam"
 
     def press(self, parent):
-        parent.compute_segmentation(model_name=self.model_name)
+        parent.compute_segmentation(model_name="cpsam")
 
 
 class FilterButton(QPushButton):

cellpose/models.py

@@ -470,4 +470,4 @@ def _compute_masks(self, shape, dP, cellprob, flow_threshold=0.4, cellprob_thres
         if shape[0] > 1:
             models_logger.info("masks created in %2.2fs" % (flow_time))
 
-        return masks
+        return masks

conftest.py

@@ -20,10 +20,10 @@ def image_names_3d():
 
 
 def extract_zip(cached_file, url, data_path):
-    utils.download_url_to_file(url, cached_file)        
-    with zipfile.ZipFile(cached_file,"r") as zip_ref:
-        zip_ref.extractall(data_path)
-
+    if not cached_file.exists():
+        utils.download_url_to_file(url, cached_file)        
+        with zipfile.ZipFile(cached_file,"r") as zip_ref:
+            zip_ref.extractall(data_path)
 
 @pytest.fixture()
 def data_dir(image_names):
@@ -96,4 +96,4 @@ def eval(self, x, **kwargs):
         toc = time.time()
 
         print(f'eval() time elapsed: {toc-tic}')
-        return res
+        return res