celldetective 1.5.0b0__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.5.0b"
+__version__ = "1.5.0b1"

celldetective/gui/InitWindow.py

@@ -256,7 +256,7 @@ class AppInitWindow(CelldetectiveMainWindow):
             DownloadProcess = self.bg_loader.DownloadProcess
         else:
             from celldetective.processes.downloader import DownloadProcess
-        from celldetective.gui.workers import ProgressWindow
+        from celldetective.gui.workers import GenericProgressWindow
 
         self.target_dir = str(
             QFileDialog.getExistingDirectory(self, "Select Folder for Download")
@@ -268,12 +268,12 @@ class AppInitWindow(CelldetectiveMainWindow):
             self.output_dir = self.target_dir
             self.file = "demo_ricm"
             process_args = {"output_dir": self.output_dir, "file": self.file}
-            self.job = ProgressWindow(
+            self.job = GenericProgressWindow(
                 DownloadProcess,
                 parent_window=self,
                 title="Download",
-                position_info=False,
                 process_args=process_args,
+                label_text="Downloading demo_ricm...",
             )
             result = self.job.exec_()
             if result == QDialog.Accepted:

celldetective/gui/workers.py

@@ -316,3 +316,102 @@ class RunnerSignal(QObject):
 
     finished = pyqtSignal()
     error = pyqtSignal(str)
+
+
+class GenericProgressWindow(CelldetectiveDialog):
+
+    def __init__(
+        self,
+        process=None,
+        parent_window=None,
+        title="",
+        process_args=None,
+        label_text="Progress:",
+    ):
+
+        super().__init__()
+
+        self.setWindowTitle(f"{title}")
+        self.__process = process
+        self.parent_window = parent_window
+
+        self.__btn_stp = QPushButton("Cancel")
+        self.__label = QLabel("Idle")
+        self.progress_label = QLabel(label_text)
+
+        self.progress_bar = QProgressBar()
+        self.progress_bar.setValue(0)
+        self.progress_bar.setFormat("%p%")
+
+        self.__runner = Runner(
+            process=self.__process,
+            process_args=process_args,
+        )
+        logger.info("Runner initialized...")
+        self.pool = QThreadPool.globalInstance()
+
+        self.__btn_stp.clicked.connect(self.__stp_net)
+        self.__runner.signals.finished.connect(self.__on_finished)
+        self.__runner.signals.error.connect(self.__on_error)
+        self.__runner.signals.update_status.connect(self.__label.setText)
+
+        # Connect update_pos for generic progress (Runner maps generic list progress to update_pos)
+        self.__runner.signals.update_pos.connect(self.progress_bar.setValue)
+
+        self.__btn_stp.setDisabled(True)
+
+        self.layout = QVBoxLayout()
+        self.layout.addWidget(self.progress_label)
+        self.layout.addWidget(self.progress_bar)
+
+        self.btn_layout = QHBoxLayout()
+        self.btn_layout.addWidget(self.__btn_stp)
+        self.btn_layout.addWidget(self.__label)
+
+        self.layout.addLayout(self.btn_layout)
+
+        self.setLayout(self.layout)
+        self.setFixedSize(QSize(400, 150))
+        self.show()
+        self.raise_()
+        self.activateWindow()
+        logger.info("GenericProgressWindow initialized and shown.")
+        self.__run_net()
+        self.setModal(True)
+
+    def closeEvent(self, evnt):
+        evnt.ignore()
+        self.setWindowState(Qt.WindowMinimized)
+
+    def __run_net(self):
+        self.__btn_stp.setEnabled(True)
+        self.__label.setText("Running...")
+        self.pool.start(self.__runner)
+
+    def __stp_net(self):
+        self.__runner.close()
+        logger.info("\n Job cancelled... Abort.")
+        self.reject()
+
+    def __on_finished(self):
+        self.__btn_stp.setDisabled(True)
+        self.__label.setText("\nFinished!")
+        self.__runner.close()
+        self.accept()
+
+    def __on_error(self, message="Error"):
+        self.__btn_stp.setDisabled(True)
+        self.__label.setText("\nError")
+        self.__runner.close()
+
+        # Show error in a message box to ensure it's seen
+        from PyQt5.QtWidgets import QMessageBox
+
+        msg = QMessageBox()
+        msg.setIcon(QMessageBox.Critical)
+        msg.setText("Process failed")
+        msg.setInformativeText(str(message))
+        msg.setWindowTitle("Error")
+        msg.exec_()
+
+        self.reject()

celldetective/processes/downloader.py

@@ -11,101 +11,127 @@ import time
 from pathlib import Path
 import json
 
+
 class DownloadProcess(Process):
 
-	def __init__(self, queue=None, process_args=None, *args, **kwargs):
-		
-		super().__init__(*args, **kwargs)
-		
-		if process_args is not None:
-			for key, value in process_args.items():
-				setattr(self, key, value)
-
-		self.queue = queue
-		self.progress = True
-
-		file_path = Path(os.path.dirname(os.path.realpath(__file__)))
-		zenodo_json = os.sep.join([str(file_path.parents[2]),"celldetective", "links", "zenodo.json"])
-		print(f"{zenodo_json=}")
-		
-		with open(zenodo_json,"r") as f:
-			zenodo_json = json.load(f)
-		all_files = list(zenodo_json['files']['entries'].keys())
-		all_files_short = [f.replace(".zip","") for f in all_files]
-		zenodo_url = zenodo_json['links']['files'].replace('api/','')
-		full_links = ["/".join([zenodo_url, f]) for f in all_files]
-		index = all_files_short.index(self.file)
-		
-		self.zip_url = full_links[index]
-		self.path_to_zip_file = os.sep.join([self.output_dir, 'temp.zip'])
-
-		self.sum_done = 0
-		self.t0 = time.time()
-
-	def download_url_to_file(self, url, dst):
-		try:
-			file_size = None
-			ssl._create_default_https_context = ssl._create_unverified_context
-			u = urlopen(url)
-			meta = u.info()
-			if hasattr(meta, 'getheaders'):
-				content_length = meta.getheaders("Content-Length")
-			else:
-				content_length = meta.get_all("Content-Length")
-			if content_length is not None and len(content_length) > 0:
-				file_size = int(content_length[0])
-			# We deliberately save it in a temp file and move it after
-			dst = os.path.expanduser(dst)
-			dst_dir = os.path.dirname(dst)
-			f = tempfile.NamedTemporaryFile(delete=False, dir=dst_dir)
-
-			try:
-				with tqdm(total=file_size, disable=not self.progress,
-						  unit='B', unit_scale=True, unit_divisor=1024) as pbar:
-					while True:
-						buffer = u.read(8192) #8192
-						if len(buffer) == 0:
-							break
-						f.write(buffer)
-						pbar.update(len(buffer))
-						self.sum_done+=len(buffer) / file_size * 100
-						mean_exec_per_step = (time.time() - self.t0) / (self.sum_done*file_size / 100 + 1)
-						pred_time = (file_size - (self.sum_done*file_size / 100 + 1)) * mean_exec_per_step
-						self.queue.put([self.sum_done, pred_time])
-				f.close()
-				shutil.move(f.name, dst)
-			finally:
-				f.close()
-				if os.path.exists(f.name):
-					os.remove(f.name)
-		except Exception as e:
-			print("No internet connection: ", e)
-			return None
-
-	def run(self):
-		
-		self.download_url_to_file(fr"{self.zip_url}",self.path_to_zip_file)
-		with zipfile.ZipFile(self.path_to_zip_file, 'r') as zip_ref:
-			zip_ref.extractall(self.output_dir)
-		
-		file_to_rename = glob(os.sep.join([self.output_dir,self.file,"*[!.json][!.png][!.h5][!.csv][!.npy][!.tif][!.ini]"]))
-		if len(file_to_rename)>0 and not file_to_rename[0].endswith(os.sep) and not self.file.startswith('demo'):
-			os.rename(file_to_rename[0], os.sep.join([self.output_dir,self.file,self.file]))
-
-		os.remove(self.path_to_zip_file)
-		self.queue.put([100,0])
-		time.sleep(0.5)
-
-		# Send end signal
-		self.queue.put("finished")
-		self.queue.close()
-
-	def end_process(self):
-
-		self.terminate()
-		self.queue.put("finished")
-
-	def abort_process(self):
-		
-		self.terminate()
-		self.queue.put("error")
+    def __init__(self, queue=None, process_args=None, *args, **kwargs):
+
+        super().__init__(*args, **kwargs)
+
+        if process_args is not None:
+            for key, value in process_args.items():
+                setattr(self, key, value)
+
+        self.queue = queue
+        self.progress = True
+
+        # Get celldetective package root
+        current_dir = os.path.dirname(os.path.realpath(__file__))
+        package_root = os.path.dirname(current_dir)
+        zenodo_json = os.path.join(package_root, "links", "zenodo.json")
+        # print(f"{zenodo_json=}")
+
+        with open(zenodo_json, "r") as f:
+            zenodo_json = json.load(f)
+        all_files = list(zenodo_json["files"]["entries"].keys())
+        all_files_short = [f.replace(".zip", "") for f in all_files]
+        zenodo_url = zenodo_json["links"]["files"].replace("api/", "")
+        full_links = ["/".join([zenodo_url, f]) for f in all_files]
+        index = all_files_short.index(self.file)
+
+        self.zip_url = full_links[index]
+        self.path_to_zip_file = os.sep.join([self.output_dir, "temp.zip"])
+
+        self.sum_done = 0
+        self.t0 = time.time()
+
+    def download_url_to_file(self, url, dst):
+        try:
+            file_size = None
+            ssl._create_default_https_context = ssl._create_unverified_context
+            u = urlopen(url)
+            meta = u.info()
+            if hasattr(meta, "getheaders"):
+                content_length = meta.getheaders("Content-Length")
+            else:
+                content_length = meta.get_all("Content-Length")
+            if content_length is not None and len(content_length) > 0:
+                file_size = int(content_length[0])
+            # We deliberately save it in a temp file and move it after
+            dst = os.path.expanduser(dst)
+            dst_dir = os.path.dirname(dst)
+            f = tempfile.NamedTemporaryFile(delete=False, dir=dst_dir)
+
+            try:
+                with tqdm(
+                    total=file_size,
+                    disable=not self.progress,
+                    unit="B",
+                    unit_scale=True,
+                    unit_divisor=1024,
+                ) as pbar:
+                    while True:
+                        buffer = u.read(8192)  # 8192
+                        if len(buffer) == 0:
+                            break
+                        f.write(buffer)
+                        pbar.update(len(buffer))
+                        self.sum_done += len(buffer) / file_size * 100
+                        mean_exec_per_step = (time.time() - self.t0) / (
+                            self.sum_done * file_size / 100 + 1
+                        )
+                        pred_time = (
+                            file_size - (self.sum_done * file_size / 100 + 1)
+                        ) * mean_exec_per_step
+                        self.queue.put([self.sum_done, pred_time])
+                f.close()
+                shutil.move(f.name, dst)
+            finally:
+                f.close()
+                if os.path.exists(f.name):
+                    os.remove(f.name)
+        except Exception as e:
+            print("No internet connection: ", e)
+            return None
+
+    def run(self):
+
+        self.download_url_to_file(rf"{self.zip_url}", self.path_to_zip_file)
+        with zipfile.ZipFile(self.path_to_zip_file, "r") as zip_ref:
+            zip_ref.extractall(self.output_dir)
+
+        file_to_rename = glob(
+            os.sep.join(
+                [
+                    self.output_dir,
+                    self.file,
+                    "*[!.json][!.png][!.h5][!.csv][!.npy][!.tif][!.ini]",
+                ]
+            )
+        )
+        if (
+            len(file_to_rename) > 0
+            and not file_to_rename[0].endswith(os.sep)
+            and not self.file.startswith("demo")
+        ):
+            os.rename(
+                file_to_rename[0], os.sep.join([self.output_dir, self.file, self.file])
+            )
+
+        os.remove(self.path_to_zip_file)
+        self.queue.put([100, 0])
+        time.sleep(0.5)
+
+        # Send end signal
+        self.queue.put("finished")
+        self.queue.close()
+
+    def end_process(self):
+
+        self.terminate()
+        self.queue.put("finished")
+
+    def abort_process(self):
+
+        self.terminate()
+        self.queue.put("error")

celldetective/utils/downloaders.py

@@ -159,6 +159,44 @@ def download_url_to_file(url, dst, progress=True):
 def download_zenodo_file(file, output_dir):
 
     logger.info(f"{file=} {output_dir=}")
+
+    # GUI Check
+    try:
+        from PyQt5.QtWidgets import QApplication, QDialog
+
+        app = QApplication.instance()
+        use_gui = app is not None
+    except ImportError:
+        use_gui = False
+
+    if use_gui:
+        try:
+            from celldetective.gui.workers import GenericProgressWindow
+            from celldetective.processes.downloader import DownloadProcess
+
+            # Find parent window if possible, else None is fine for a dialog
+            parent = app.activeWindow()
+
+            process_args = {"output_dir": output_dir, "file": file}
+            job = GenericProgressWindow(
+                DownloadProcess,
+                parent_window=parent,
+                title="Download",
+                process_args=process_args,
+                label_text=f"Downloading {file}...",
+            )
+            result = job.exec_()
+            if result == QDialog.Accepted:
+                return  # DownloadProcess handles the file operations
+            else:
+                logger.info("Download cancelled or failed.")
+                return
+
+        except Exception as e:
+            logger.error(f"Failed to use GUI downloader: {e}. Falling back to console.")
+            # Fallback to console implementation below if GUI fails
+
+    # Console Implementation
     zenodo_json = os.sep.join(
         [
             os.path.split(os.path.dirname(os.path.realpath(__file__)))[0],

{celldetective-1.5.0b0.dist-info → celldetective-1.5.0b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b0
+Version: 1.5.0b1
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.5.0b0.dist-info → celldetective-1.5.0b1.dist-info}/RECORD

@@ -1,6 +1,6 @@
 celldetective/__init__.py,sha256=LfnOyfUnYPGDc8xcsF_PfYEL7-CqAb7BMBPBIWGv84o,666
 celldetective/__main__.py,sha256=Rzzu9ArxZSgfBVjV-lyn-3oanQB2MumQR6itK5ZaRpA,2597
-celldetective/_version.py,sha256=AMZ674Vi7YVfxguQYyBETUqhTbHYuk3GDM_LK-X1UBg,23
+celldetective/_version.py,sha256=6QH0Vgfkt-TPgdS6Nql1G9jeZAByFTkMEeYsa6NspPk,24
 celldetective/events.py,sha256=n15R53c7QZ2wT8gjb0oeNikQbuRBrVVbyNsRCqXjzXA,8166
 celldetective/exceptions.py,sha256=f3VmIYOthWTiqMEV5xQCox2rw5c5e7yog88h-CcV4oI,356
 celldetective/extra_properties.py,sha256=s_2R4_El2p-gQNZ_EpgDxgrN3UnRitN7KDKHhyLuoHc,21681
@@ -15,7 +15,7 @@ celldetective/signals.py,sha256=2UURVmeonNgUHpiMQVSps0E9VuskKSbsfsmeCtEmfp8,1374
 celldetective/tracking.py,sha256=pjejp65IltUMjW_tlbxjYW0SoBR1-gaEeSJa0y2cWpw,49286
 celldetective/datasets/segmentation_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/datasets/signal_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-celldetective/gui/InitWindow.py,sha256=ynelHEkC9USY14MrsHr_HKtC6YPWQOahk3sv-ZcaKFc,20921
+celldetective/gui/InitWindow.py,sha256=fNuY7d8EtNNOB2_ZrijyNdoQ7x5GOlq1IFqPBUv1ElM,20953
 celldetective/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/gui/about.py,sha256=l9SA7WnQs3ISPvZYAGMmf1A0GRXcinkyGwWJpG8akFQ,1977
 celldetective/gui/analyze_block.py,sha256=R82PVFHXfKn8BvUCpbjDOkLBNF4xRVCzYKFHitjw0kk,4114
@@ -39,7 +39,7 @@ celldetective/gui/seg_model_loader.py,sha256=6DzpX630JJgtcsaDEuWA8PEkeb8FC3p__3x
 celldetective/gui/survival_ui.py,sha256=IwdRm1gRvhkWdMtrQk04OIKKksW3NZSGYtZO_2GptrA,16034
 celldetective/gui/tableUI.py,sha256=kZP2lp9NwHtbWEqIyaDwohX42tRkhI0Hlf_8O5w5BD0,61267
 celldetective/gui/thresholds_gui.py,sha256=w6ke2TyIEi71LxbuFGz0UrwH8h21N_ESU-o6xq_NNKo,33346
-celldetective/gui/workers.py,sha256=0U-wn_dmZjB2idGjpM8s_1dLET9Eh2TmVWB6PLJTSas,11411
+celldetective/gui/workers.py,sha256=6uk4skcwNd3qowBrpSSgv0hvbL-4naH-g-TmF3u7NB4,14363
 celldetective/gui/base/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/gui/base/channel_norm_generator.py,sha256=JqNAo87zA3nMKzkGjvoeV-SHI89eIATwQj4jHv3-LpI,13973
 celldetective/gui/base/components.py,sha256=DF1sT2AZIpTec7mYYihIMTDYKRrT5k2DoaceZjvAEEw,7452
@@ -118,7 +118,7 @@ celldetective/processes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG
 celldetective/processes/background_correction.py,sha256=fyv2_7ztUex7RDwIRaURweYZsRe-YD_ZPUHeiFmVq6Q,10715
 celldetective/processes/compute_neighborhood.py,sha256=DGi4U3el0OisRNaOQSzUaXpEgHBO440-Q4cUphB6FAA,34393
 celldetective/processes/detect_events.py,sha256=4psWjnYxbMB3p0BrRoQgkXgIdsnUIErrqUkE9CU4hRM,9733
-celldetective/processes/downloader.py,sha256=jnNitmQ9xUCGJHSvr3Myts5soe6rdYDBx_AGJKr1AWk,3406
+celldetective/processes/downloader.py,sha256=3SA5T1AoLch90d-VZzIY4wVAlSjDY_kgVLPN3ztRyVk,4589
 celldetective/processes/measure_cells.py,sha256=ccf2j7_6dcRevEhseVXioIjiATx8IvIsi5ZG3IcdhJY,20876
 celldetective/processes/segment_cells.py,sha256=klGl5y3tHbLbQFNAQz0PV1FspmiPC-GHVGWYLgyLqwc,26500
 celldetective/processes/track_cells.py,sha256=cgQNn7fsqPCHODhe27sqvMUlubsi7qM_0qjAXbj68oY,15084
@@ -141,7 +141,7 @@ celldetective/utils/color_mappings.py,sha256=yarqOTSrTsnOPPiPrrN_vLoPCbgWqF3wjqF
 celldetective/utils/data_cleaning.py,sha256=K-2gScxLreX7QkrM0h3dZdP0IsmvCzcxNh2-M9PALZY,22025
 celldetective/utils/data_loaders.py,sha256=tExtC_7gX16VYmYFz8BU7jRKLDug2egVghU1YIcGRh0,16292
 celldetective/utils/dataset_helpers.py,sha256=3ezpHO6nytw2Mx0D3maP_4535V2ohOTQn6Qpfk8gnms,6898
-celldetective/utils/downloaders.py,sha256=Cf7K-f_Bm4M6HIfgiSoIoph0O1NS6LZIaYvgWKauXes,6595
+celldetective/utils/downloaders.py,sha256=BIl_8XCeaKvtMVC36WITT2g5-O-n0csoMEQXVoa1B4o,7887
 celldetective/utils/experiment.py,sha256=bgADS70QuW4KGbzDJbVpVM-tw4qmZKMWtDT1cSxugrY,58342
 celldetective/utils/image_augmenters.py,sha256=USYd8z6dVn5z1x96IYJ4mG0smN9I_S21QMGU0wyHmjc,11654
 celldetective/utils/image_cleaning.py,sha256=KliQ3K5hdwPx4eFxJnmg3yi-ZIoimEveunPJkbbA6wA,2388
@@ -164,7 +164,7 @@ celldetective/utils/event_detection/__init__.py,sha256=KX20PwPTevdbZ-25otDy_QTme
 celldetective/utils/plots/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/utils/plots/regression.py,sha256=oUCn29-hp7PxMqC-R0yoL60KMw5ZWpZAIoCDh2ErlcY,1764
 celldetective/utils/stardist_utils/__init__.py,sha256=e9s3DEaTKCUOGZb5k_DgShBTl4B0U-Jmg3Ioo8D5PyE,3978
-celldetective-1.5.0b0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.5.0b1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
 tests/test_filters.py,sha256=uj4NVyUnKXa18EpTSiWCetGKI1VFopDyNSJSUxX44wA,1689
@@ -180,8 +180,8 @@ tests/test_utils.py,sha256=aSB_eMw9fzTsnxxdYoNmdQQRrXkWqBXB7Uv4TGU6kYE,4778
 tests/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/gui/test_new_project.py,sha256=wRjW2vEaZb0LWT-f8G8-Ptk8CW9z8-FDPLpV5uqj6ck,8778
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