SPACEtomo 1.2.0__py3-none-any.whl

SPACEtomo/CLI.py

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+#!/usr/bin/env python
+# ===================================================================
+# ScriptName:   CLI
+# Purpose:      User interface for inspecting and labeling lamella grid atlases collected with SPACEtomo.
+#               More information at http://github.com/eisfabian/SPACEtomo
+# Author:       Fabian Eisenstein
+# Created:      2024/04/26
+# Revision:     v1.2
+# Last Change:  2024/07/18: reworked GUI to class
+# #             2024/06/07: added lamella table row highlighting, added save coords in YOLO format
+#               2024/06/05: introduced Menu class, added shortcuts for most buttons
+#               2024/06/04: added pix size check for export, added rescaling of mrc file
+#               2024/06/03: added include empty tiles option, added save json option
+#               2024/05/31: added status line, fixed tiles bounds, added next button, added hide/showElements
+#               2024/05/30: added rescaling, saving as png, fixed export tiles
+#               2024/05/29: outsourced plot clearing
+#               2024/05/23: added lamella labels on plot, added padding when exporting edge tiles, fixed plotTiles
+#               2024/05/10: added reading and writing of YOLO format labels, added saving of tiles with labels, added map class
+#               2024/05/02: added lamella color from config, added reset zoom, delegated plot generation, call lamella detection
+#               2024/04/30: added lamella focus buttons, outline scaling, list sorting
+#               2024/04/26: Copy most of SPACEtomo_tgt
+# ===================================================================
+
+import sys
+try:
+    import dearpygui.dearpygui as dpg
+except ModuleNotFoundError:
+    print("WARNING: GUI library is not installed.")
+import argparse
+import shutil
+from pathlib import Path
+
+from SPACEtomo.modules.utils import log
+from SPACEtomo.modules.gui.lam_sel import LamellaGUI
+from SPACEtomo.modules.gui.tgt_sel import TargetGUI
+
+# Attempt SerialEM import
+import SPACEtomo.config as config
+sys.path.insert(len(sys.path), config.SERIALEM_PYTHON_PATH)
+try:
+    import serialem as sem
+    SERIALEM = True
+except ModuleNotFoundError:
+    SERIALEM = False
+
+def show(gui, path=""):
+    dpg.create_context()
+    main = gui(path)
+    main.show()
+    dpg.destroy_context()
+    
+def run_process(process):
+    log(f"Starting {process}...")
+    process()
+    
+def main():
+    # Process arguments
+    parser = argparse.ArgumentParser(description="Command line interface for different SPACEtomo functions (e.g. GUIs).")
+    parser.add_argument("task", type=str, default="targets", help="Name of the SPACEtomo task to run. Options: targets -> Open target selection GUI | lamella -> Open lamella selection GUI | run -> Start SPACEtomo run | scripts -> Get copy of SerialEM scripts")
+    parser.add_argument("map_file", nargs="?", type=str, default="", help="Absolute path to a map file to load in GUI [.png].")
+    args = parser.parse_args()
+
+    # Get GUI
+    gui = None
+    process = None
+    if args.task.lower() == "targets" or args.task.lower() == "target":
+        gui = TargetGUI
+    elif args.task.lower() == "lamella" or args.task.lower() == "lamellae":
+        gui = LamellaGUI
+    elif args.task.lower() == "run":
+        if SERIALEM:
+            from SPACEtomo import run
+            process = run.main
+        else:
+            log(f"ERROR: SPACEtomo {args.task} requires SerialEM!")
+    elif args.task.lower() == "scripts":
+        serialem_script_dir = Path(__file__).parent / "SerialEM_scripts"
+        target_path = Path.cwd() / "SerialEM_scripts"
+        if not target_path.exists():
+            shutil.copytree(serialem_script_dir, target_path)
+            (target_path / "__init__.py").unlink()
+            log(f"SerialEM scripts were successfully copied to: {target_path}")
+        else:
+            log(f"ERROR: A folder named SerialEM_scripts already exists!")
+    else:
+        raise ValueError(f"No task found with name {args.task}!")
+
+    # Check map file
+    if gui:
+        map_file = ""
+        if args.map_file != "": 
+            map_file = Path(args.map_file)
+            if not map_file.exists():
+                map_file = ""
+                log("WARNING: Map file does not exist! Attempting to start task without map...")            
+    
+        # Run GUI
+        show(gui, map_file)
+        
+    if process:
+        run_process(process)
+
+
+if __name__ == "__main__":
+    main()

SPACEtomo/GUI.py

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+#!/usr/bin/env python
+# ===================================================================
+# ScriptName:   GUI
+# Purpose:      User interface for inspecting and labeling lamella grid atlases collected with SPACEtomo.
+#               More information at http://github.com/eisfabian/SPACEtomo
+# Author:       Fabian Eisenstein
+# Created:      2024/04/26
+# Revision:     v1.2
+# Last Change:  2024/07/18: reworked GUI to class
+# #             2024/06/07: added lamella table row highlighting, added save coords in YOLO format
+#               2024/06/05: introduced Menu class, added shortcuts for most buttons
+#               2024/06/04: added pix size check for export, added rescaling of mrc file
+#               2024/06/03: added include empty tiles option, added save json option
+#               2024/05/31: added status line, fixed tiles bounds, added next button, added hide/showElements
+#               2024/05/30: added rescaling, saving as png, fixed export tiles
+#               2024/05/29: outsourced plot clearing
+#               2024/05/23: added lamella labels on plot, added padding when exporting edge tiles, fixed plotTiles
+#               2024/05/10: added reading and writing of YOLO format labels, added saving of tiles with labels, added map class
+#               2024/05/02: added lamella color from config, added reset zoom, delegated plot generation, call lamella detection
+#               2024/04/30: added lamella focus buttons, outline scaling, list sorting
+#               2024/04/26: Copy most of SPACEtomo_tgt
+# ===================================================================
+
+import sys
+from SPACEtomo.modules.utils import log
+try:
+    import dearpygui.dearpygui as dpg
+except:
+    log("ERROR: DearPyGUI module not installed! If you cannot install it, please run the target selection GUI from an external machine.")
+    sys.exit()
+import argparse
+from pathlib import Path
+from SPACEtomo.modules.gui.lam_sel import LamellaGUI
+from SPACEtomo.modules.gui.tgt_sel import TargetGUI
+
+def run_process(gui, path="", auto_close=False):
+    dpg.create_context()
+    main = gui(path, auto_close=auto_close)
+    main.show()
+    dpg.destroy_context()
+    
+def main():
+    # Process arguments
+    parser = argparse.ArgumentParser(description="Calls GUI to inspect whole grid maps and detected lamellae.")
+    parser.add_argument("gui", type=str, default="targets", help="Name of GUI to be opened. Options: targets, lamella")
+    parser.add_argument("map_file", nargs="?", type=str, default="", help="Absolute path to a map [.png].")
+    parser.add_argument("--auto_close", action="store_true", help="Auto-close GUI after inspection.")
+    args = parser.parse_args()
+
+    # Get GUI
+    if args.gui == "targets":
+        gui = TargetGUI
+    elif args.gui == "lamella":
+        gui = LamellaGUI
+    else:
+        raise ValueError(f"No GUI found with name {args.gui}!")
+
+    # Check map file
+    map_file = ""
+    if args.map_file != "": 
+        map_file = Path(args.map_file)
+        if not map_file.exists():
+            map_file = ""
+            log("WARNING: Map file does not exist! Attempting to open GUI without map...")
+
+    # Run GUI
+    run_process(gui, map_file, args.auto_close)
+    
+
+if __name__ == "__main__":
+    main()

SPACEtomo/SerialEM_scripts/SPACEtomo_lamellaDetectionGUI.py

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+#!Python
+# ===================================================================
+#ScriptName SPACEtomo_lamellaDetectionGUI
+# Purpose:      Script to start SPACEtomo lamella detection GUI.
+#               More information at http://github.com/eisfabian/SPACEtomo
+# Author:       Fabian Eisenstein
+# ===================================================================
+
+import serialem as sem
+import sys
+from SPACEtomo.modules.utils import log
+try:
+    import dearpygui.dearpygui as dpg
+except:
+    log("ERROR: DearPyGUI module not installed! If you cannot install it, please run the target selection GUI from an external machine.")
+    sys.exit()
+
+from SPACEtomo.modules.gui.lam_sel import LamellaGUI
+
+def main():
+    dpg.create_context()
+    main = LamellaGUI()
+    main.show()
+    dpg.destroy_context()
+
+if __name__ == "__main__":
+    main()

SPACEtomo/SerialEM_scripts/SPACEtomo_postAction.py

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+#!Python
+# ===================================================================
+#ScriptName SPACEtomo_postAction
+# Purpose:      Post action script to setup targets from SPACEtomo runs.
+#               More information at http://github.com/eisfabian/SPACEtomo
+# Author:       Fabian Eisenstein
+# ===================================================================
+
+import serialem as sem
+from SPACEtomo.run_postaction import main
+
+main()

SPACEtomo/SerialEM_scripts/SPACEtomo_run.py

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+#!Python
+# ===================================================================
+#ScriptName SPACEtomo
+# Purpose:      Finds lamellae in grid map, collects lamella montages and finds targets using deep learning models.
+#               More information at http://github.com/eisfabian/PACEtomo
+# Author:       Fabian Eisenstein
+# Created:      2023/05/31
+# ===================================================================
+
+### TODO before running:
+# - Microscope alignments
+# - Run inventory and name grids in autoloader
+# - Low Dose mode setup (ensure that both WG image state and MM (Low Dose) image states produce good images)
+# - Set Shift offset between Record and View mag and check if "High Def IS" calibrations are necessary (Apply large IS in View and check if Record acquires at same position)
+# - PACEtomo preparation and script settings (for automation level 5)
+# - Setup "Acquire at Items" dialogue to run PACEtomo as main action and SPACEtomo_postAction as "Run after primary action" (for automation level 5)
+# - In case of inference on an external GPU workstation, start SPACEtomo_monitor.py script and set external_map_dir accordingly
+###
+
+############ SETTINGS ############ 
+
+automation_level        = 4                     # = 1: collect WG map and find lamellae
+                                                # = 2: collect MM maps for each lamella
+                                                # = 3: segment lamella MM maps
+                                                # = 4: setup targets based on segmentation for each lamella
+                                                # = 5: start PACEtomo batch acquisition of all targets
+
+
+
+script_numbers          = [10, 11, 13]          # Numbers of [SPACEtomo_run.py, SPACEtomo_postAction.py, PACEtomo.py] scripts in SerialEM script editor
+external_map_dir        = ""                    # Path to directory where maps are saved and segmentations are expected (run "SPACEmonitor" on external machine to manage runs and queue)
+
+# Grid settings [Level 1]
+
+grid_list               = [1]                   # Number or list of numbers of target grid(s) in autoloader
+exclude_lamella_classes = ["gone"]              # Lamella classes to exclude, possible classes: ["broken", "gone", "thick", "wedge", "contaminated", "good"]
+
+WG_image_state          = 1                     # Imaging state name or index for whole grid montage (set up before!)
+IM_mag_index            = 10                    # Intermediate mag index to use (10: 580x) 
+WG_distance_threshold   = 5                     # Minimum distance [microns] between lamellae to not be considered duplicate detection
+
+WG_wait_for_inspection  = False                 # = True: wait for inspection of lamellae detection by operator using the GUI
+
+# Lamella montage settings [Level 2]
+
+MM_image_state          = [13]                  # Imaging state name or index for Low Dose Mode, this can be several imaging states to specify Record, View, ... (set up before!)
+
+# Targeting settings [Level 4]
+
+manual_selection        = False                 # = True: creates empty segmentation, allows for manual target setup by operator using the GUI
+MM_wait_for_inspection  = False                 # = True: wait for inspection of targets using the GUI
+
+target_list             = ["mitos"]             # List of target classes, additive, possible classes: ["background", "white", "black", "crack", "coating", "cell", "cellwall", "nucleus", "vacuole", "mitos", "lipiddroplets", "vesicles", "multivesicles", "membranes", "dynabeads", "ice", "cryst", "lamella"]
+avoid_list              = ["black", "white", "ice", "crack", "dynabeads"]    # list of classes to avoid, additive
+target_score_threshold  = 0.01                  # Weighted fraction of FOV containing the target, keep at 0 for any structures smaller than the FOV
+sparse_targets          = True                  # Use for sparse targets on the sample (e.g. mitos, vesicles)
+target_edge             = False                 # Use for edge targets (e.g. nuclear envelope, cell periphery)
+penalty_weight          = 0.3                   # Factor to downweight overlap with classes to avoid
+
+extra_tracking          = False                 # Add an extra center target for the tracking tilt series (not working properly yet)
+max_tilt                = 60                    # Maximum tilt angle [degrees] of tilt series to be acquired 
+
+########## END SETTINGS ########## 
+
+try:
+    import serialem as sem
+except ModuleNotFoundError:
+    print("WARNING: Trying to run SerialEM externally!")
+
+from SPACEtomo.run import main
+import SPACEtomo.modules.utils as utils
+
+cur_dir = utils.getCurDir()
+utils.saveSettings(cur_dir / "SPACEtomo_settings.ini", globals())
+main()

SPACEtomo/SerialEM_scripts/SPACEtomo_targetSelectionGUI.py

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+#!Python
+# ===================================================================
+#ScriptName SPACEtomo_targetSelectionGUI
+# Purpose:      Script to start SPACEtomo target selection GUI.
+#               More information at http://github.com/eisfabian/SPACEtomo
+# Author:       Fabian Eisenstein
+# ===================================================================
+
+import serialem as sem
+import sys
+from SPACEtomo.modules.utils import log
+try:
+    import dearpygui.dearpygui as dpg
+except:
+    log("ERROR: DearPyGUI module not installed! If you cannot install it, please run the target selection GUI from an external machine.")
+    sys.exit()
+from pathlib import Path
+
+from SPACEtomo.modules import utils
+from SPACEtomo.modules.gui.tgt_sel import TargetGUI
+
+def run(path=""):
+    dpg.create_context()
+    main = TargetGUI(path)
+    main.show()
+    dpg.destroy_context()
+
+def main():
+    # Look for SPACE_maps
+    cur_dir = utils.getCurDir()
+    space_maps = sorted(cur_dir.glob("**/SPACE_maps"))
+    print(space_maps)
+    if len(space_maps) > 0:
+        run(space_maps[0])
+    else:
+        utils.log(f"ERROR: No SPACE_maps directory found within current directory [{cur_dir}]!")
+
+if __name__ == "__main__":
+    main()

SPACEtomo/__init__.py

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+__version__ = "1.2.0"
+version_SerialEM = ("40200", "20240317")

SPACEtomo/config.py

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+#!/usr/bin/env python
+# ===================================================================
+# ScriptName:   SPACEtomo_config
+# Purpose:      Configurations for deep learning models used in SPACEtomo.
+#               More information at http://github.com/eisfabian/SPACEtomo
+# Author:       Fabian Eisenstein
+# Created:      2023/10/04
+# Revision:     v1.2
+# Last Change:  2024/12/13: added check for backup config
+#               2024/09/26: outsourcing of more settings from SPACEtomo_run scripts
+#               2024/08/20: added SerialEM connection setting
+#               2024/05/02: changed model colors to RGBA
+#               2024/03/12: removed max_runs
+#               2023/10/04: outsourcing of settings from main SPACEtomo script
+# ===================================================================
+
+# SerialEM specific settings
+SERIALEM_IP = "127.0.0.1"
+SERIALEM_PORT = 48888
+SERIALEM_PYTHON_PATH = "C:/Program Files/SerialEM/PythonModules"
+
+DUMMY = False
+DEBUG = False
+
+# Acquisition settings
+WG_montage_overlap      = 0.15                  # overlap between pieces of whole grid montage
+WG_detection_threshold  = 0.1                   # confidence threshold for lamella acceptance
+
+MM_montage_overlap      = 0.25                  # overlap between pieces of medium mag montage
+MM_padding_factor       = 1.5                   # padding of estimated lamella size for medium mag montage
+
+aperture_control        = True                  # set to True if SerialEM can control apertures (https://bio3d.colorado.edu/SerialEM/hlp/html/setting_up_serialem.htm#apertures)
+objective_aperture      = 70                    # diameter of objective aperture
+
+# Target selection settings
+max_iterations          = 10                    # maximum number of iterations for target placement optimization
+
+# Model specific settings (depend on how the model was trained)
+
+# WG model (YOLOv8)
+WG_model_file = 'model.pt'
+WG_model_pix_size = 400.0 # nm/px
+WG_model_sidelen = 1024 # px
+WG_model_categories = ["broken",           "contaminated",     "good",             "thick",            "wedge",             "gone"          ] 
+WG_model_gui_colors = [(255, 125, 0, 255), (255, 215, 0, 255), (50, 150, 50, 255), (59, 92, 128, 255), (87, 138, 191, 255), (200, 0, 0, 255)]
+WG_model_nav_colors = [0,                  3,                  1,                  2,                  2,                   0               ]
+
+# Category name     Description                                                         Color
+# ----------------- ------------------------------------------------------------------- ----------
+# good:             intact lamellae with good thickness                                 green (1)
+# thick:            dark lamellae                                                       blue (2)
+# wedge/unfinished: lamellae that are good on one end but thick on other end            blue (2)
+# contaminated:     lamellae with visible ice blobs                                     yellow (3)
+# broken:           lamella with crack, only parts remaining, only one side attached    orange (0)
+# gone:             trench without lamella                                              red (0)
+
+# MM model (nnUNet)
+MM_model_script = "run_nnUNet.py"
+MM_model_folder = 'model'
+MM_model_folds = [0, 1, 2, 3, 4]
+MM_model_pix_size = 22.83 / 10  # nm/px
+
+#######################################
+# Self-check
+import sys
+import shutil
+from pathlib import Path
+
+config_backup = Path(__file__).parent / "models" / "config.py"
+if config_backup.exists():
+    from SPACEtomo.models import config as backup
+    if WG_model_file != backup.WG_model_file or MM_model_folder != backup.MM_model_folder:
+        print(f"WARNING: Loading backup config file from previous SPACEtomo version. Please run the command/script again!")
+        shutil.copy(config_backup, __file__)
+        sys.exit()
+
+if Path(WG_model_file).exists():
+    NO_WG_MODEL = False
+else:
+    NO_WG_MODEL = True
+
+if Path(MM_model_folder).exists():
+    NO_MM_MODEL = False
+else:
+    NO_MM_MODEL = True