spacr 0.0.1__py3-none-any.whl → 0.0.2__py3-none-any.whl

spacr/__init__.py

@@ -11,9 +11,11 @@ from . import timelapse
 from . import train
 from . import mask_app
 from . import annotate_app
+from . import graph_learning
 from . import gui_utils
 from . import gui_mask_app
 from . import gui_measure_app
+from . import gui_classify_app
 from . import logger
 
 __all__ = [
@@ -26,10 +28,12 @@ __all__ = [
     "timelapse",
     "train",
     "annotate_app",
+    "graph_learning",
     "gui_utils",
     "mask_app",
     "gui_mask_app",
     "gui_measure_app",
+    "gui_classify_app",
     "logger"
 ]
 

spacr/alpha.py

@@ -0,0 +1,18 @@
+def gui_mask():
+    from .cli import get_arg_parser
+    from .version import version_str
+
+    args = get_arg_parser().parse_args()
+    
+    if args.version:
+        print(version_str)
+        return
+
+    if args.headless:
+        settings = {}
+        spacr.core.preprocess_generate_masks(settings['src'], settings=settings, advanced_settings={})
+        return
+
+    global vars_dict, root
+    root, vars_dict = initiate_mask_root(1000, 1500)
+    root.mainloop()

spacr/cli.py

@@ -4,200 +4,38 @@ Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer a
 
 import argparse
 
+import argparse
+
 
 def get_arg_parser():
-    """ Parses command line arguments for cellpose main function
+    """ Parses command line arguments for spacr main functions
 
     Note: this function has to be in a separate file to allow autodoc to work for CLI.
     The autodoc_mock_imports in conf.py does not work for sphinx-argparse sometimes,
     see https://github.com/ashb/sphinx-argparse/issues/9#issue-1097057823
     """
-
-    parser = argparse.ArgumentParser(description="Cellpose Command Line Parameters")
-
-    # misc settings
-    parser.add_argument("--version", action="store_true",
-                        help="show cellpose version info")
-    parser.add_argument(
-        "--verbose", action="store_true",
-        help="show information about running and settings and save to log")
-    parser.add_argument("--Zstack", action="store_true", help="run GUI in 3D mode")
-
-    # settings for CPU vs GPU
+    
+    parser = argparse.ArgumentParser(description="SPACR Mask App Command Line Parameters")
     hardware_args = parser.add_argument_group("Hardware Arguments")
-    hardware_args.add_argument("--use_gpu", action="store_true",
-                               help="use gpu if torch with cuda installed")
-    hardware_args.add_argument(
-        "--gpu_device", required=False, default="0", type=str,
-        help="which gpu device to use, use an integer for torch, or mps for M1")
-    hardware_args.add_argument("--check_mkl", action="store_true",
-                               help="check if mkl working")
-
-    # settings for locating and formatting images
     input_img_args = parser.add_argument_group("Input Image Arguments")
-    input_img_args.add_argument("--dir", default=[], type=str,
+    #model_args = parser.add_argument_group("Model Arguments")
+    #algorithm_args = parser.add_argument_group("Algorithm Arguments")
+    #training_args = parser.add_argument_group("Training Arguments")
+    #output_args = parser.add_argument_group("Output Arguments")
+    
+    # misc settings
+    parser.add_argument("--version", action="store_true",
+                        help="show version info")
+    # misc settings
+    parser.add_argument("--headless", action="store_true",
+                        help="run the app without the gui")
+    
+    parser.add_argument("--verbose", action="store_true",
+                        help="show information about running and settings and save to log")
+    
+    hardware_args.add_argument("--gpu_device", required=False, default="0", type=str,
+                               help="which gpu device to use, use an integer for torch, or mps for M1")
+    
+    input_img_args.add_argument("--src", default=[], type=str,
                                 help="folder containing data to run or train on.")
-    input_img_args.add_argument(
-        "--image_path", default=[], type=str, help=
-        "if given and --dir not given, run on single image instead of folder (cannot train with this option)"
-    )
-    input_img_args.add_argument(
-        "--look_one_level_down", action="store_true",
-        help="run processing on all subdirectories of current folder")
-    input_img_args.add_argument("--img_filter", default=[], type=str,
-                                help="end string for images to run on")
-    input_img_args.add_argument(
-        "--channel_axis", default=None, type=int,
-        help="axis of image which corresponds to image channels")
-    input_img_args.add_argument("--z_axis", default=None, type=int,
-                                help="axis of image which corresponds to Z dimension")
-    input_img_args.add_argument(
-        "--chan", default=0, type=int, help=
-        "channel to segment; 0: GRAY, 1: RED, 2: GREEN, 3: BLUE. Default: %(default)s")
-    input_img_args.add_argument(
-        "--chan2", default=0, type=int, help=
-        "nuclear channel (if cyto, optional); 0: NONE, 1: RED, 2: GREEN, 3: BLUE. Default: %(default)s"
-    )
-    input_img_args.add_argument("--invert", action="store_true",
-                                help="invert grayscale channel")
-    input_img_args.add_argument(
-        "--all_channels", action="store_true", help=
-        "use all channels in image if using own model and images with special channels")
-
-    # model settings
-    model_args = parser.add_argument_group("Model Arguments")
-    model_args.add_argument("--pretrained_model", required=False, default="cyto",
-                            type=str,
-                            help="model to use for running or starting training")
-    model_args.add_argument("--restore_type", required=False, default=None,
-                            type=str,
-                            help="model to use for image restoration")
-    model_args.add_argument("--chan2_restore", action="store_true",
-                               help="use nuclei restore model for second channel")
-    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")
-
-    # algorithm settings
-    algorithm_args = parser.add_argument_group("Algorithm Arguments")
-    algorithm_args.add_argument(
-        "--no_resample", action="store_true", help=
-        "disable dynamics on full image (makes algorithm faster for images with large diameters)"
-    )
-    algorithm_args.add_argument(
-        "--no_interp", action="store_true",
-        help="do not interpolate when running dynamics (was default)")
-    algorithm_args.add_argument("--no_norm", action="store_true",
-                                help="do not normalize images (normalize=False)")
-    algorithm_args.add_argument(
-        "--do_3D", action="store_true",
-        help="process images as 3D stacks of images (nplanes x nchan x Ly x Lx")
-    algorithm_args.add_argument(
-        "--diameter", required=False, default=30., type=float, help=
-        "cell diameter, if 0 will use the diameter of the training labels used in the model, or with built-in model will estimate diameter for each image"
-    )
-    algorithm_args.add_argument(
-        "--stitch_threshold", required=False, default=0.0, type=float,
-        help="compute masks in 2D then stitch together masks with IoU>0.9 across planes"
-    )
-    algorithm_args.add_argument(
-        "--min_size", required=False, default=15, type=int,
-        help="minimum number of pixels per mask, can turn off with -1")
-
-    algorithm_args.add_argument(
-        "--flow_threshold", default=0.4, type=float, help=
-        "flow error threshold, 0 turns off this optional QC step. Default: %(default)s")
-    algorithm_args.add_argument(
-        "--cellprob_threshold", default=0, type=float,
-        help="cellprob threshold, default is 0, decrease to find more and larger masks")
-    algorithm_args.add_argument(
-        "--niter", default=0, type=int,
-        help="niter, number of iterations for dynamics for mask creation, default of 0 means it is proportional to diameter, set to a larger number like 2000 for very long ROIs")
-
-    algorithm_args.add_argument("--anisotropy", required=False, default=1.0, type=float,
-                                help="anisotropy of volume in 3D")
-    algorithm_args.add_argument("--exclude_on_edges", action="store_true",
-                                help="discard masks which touch edges of image")
-    algorithm_args.add_argument(
-        "--augment", action="store_true",
-        help="tiles image with overlapping tiles and flips overlapped regions to augment"
-    )
-
-    # output settings
-    output_args = parser.add_argument_group("Output Arguments")
-    output_args.add_argument(
-        "--save_png", action="store_true",
-        help="save masks as png and outlines as text file for ImageJ")
-    output_args.add_argument(
-        "--save_tif", action="store_true",
-        help="save masks as tif and outlines as text file for ImageJ")
-    output_args.add_argument("--no_npy", action="store_true",
-                             help="suppress saving of npy")
-    output_args.add_argument(
-        "--savedir", default=None, type=str, help=
-        "folder to which segmentation results will be saved (defaults to input image directory)"
-    )
-    output_args.add_argument(
-        "--dir_above", action="store_true", help=
-        "save output folders adjacent to image folder instead of inside it (off by default)"
-    )
-    output_args.add_argument("--in_folders", action="store_true",
-                             help="flag to save output in folders (off by default)")
-    output_args.add_argument(
-        "--save_flows", action="store_true", help=
-        "whether or not to save RGB images of flows when masks are saved (disabled by default)"
-    )
-    output_args.add_argument(
-        "--save_outlines", action="store_true", help=
-        "whether or not to save RGB outline images when masks are saved (disabled by default)"
-    )
-    output_args.add_argument(
-        "--save_rois", action="store_true",
-        help="whether or not to save ImageJ compatible ROI archive (disabled by default)"
-    )
-    output_args.add_argument(
-        "--save_txt", action="store_true",
-        help="flag to enable txt outlines for ImageJ (disabled by default)")
-    output_args.add_argument(
-        "--save_mpl", action="store_true",
-        help="save a figure of image/mask/flows using matplotlib (disabled by default). "
-        "This is slow, especially with large images.")
-
-    # training settings
-    training_args = parser.add_argument_group("Training Arguments")
-    training_args.add_argument("--train", action="store_true",
-                               help="train network using images in dir")
-    training_args.add_argument("--train_size", action="store_true",
-                               help="train size network at end of training")
-    training_args.add_argument("--test_dir", default=[], type=str,
-                               help="folder containing test data (optional)")
-    training_args.add_argument(
-        "--mask_filter", default="_masks", type=str, help=
-        "end string for masks to run on. use '_seg.npy' for manual annotations from the GUI. Default: %(default)s"
-    )
-    training_args.add_argument(
-        "--diam_mean", default=30., type=float, help=
-        "mean diameter to resize cells to during training -- if starting from pretrained models it cannot be changed from 30.0"
-    )
-    training_args.add_argument("--learning_rate", default=0.2, type=float,
-                               help="learning rate. Default: %(default)s")
-    training_args.add_argument("--weight_decay", default=0.00001, type=float,
-                               help="weight decay. Default: %(default)s")
-    training_args.add_argument("--n_epochs", default=500, type=int,
-                               help="number of epochs. Default: %(default)s")
-    training_args.add_argument("--batch_size", default=8, type=int,
-                               help="batch size. Default: %(default)s")
-    training_args.add_argument(
-        "--min_train_masks", default=5, type=int, help=
-        "minimum number of masks a training image must have to be used. Default: %(default)s"
-    )
-    training_args.add_argument("--SGD", default=1, type=int, help="use SGD")
-    training_args.add_argument(
-        "--save_every", default=100, type=int,
-        help="number of epochs to skip between saves. Default: %(default)s")
-    training_args.add_argument(
-        "--model_name_out", default=None, type=str,
-        help="Name of model to save as, defaults to name describing model architecture. "
-        "Model is saved in the folder specified by --dir in models subfolder.")
-
-    return parser
+    return parser