batoolset 0.1.0__tar.gz → 0.1.2__tar.gz

{batoolset-0.1.0 → batoolset-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: batoolset
-Version: 0.1.0
+Version: 0.1.2
 Summary: An aggregate of functions I find useful
 Home-page: https://github.com/baigouy/batoolset
 Author: Benoit Aigouy
@@ -15,7 +15,7 @@ License-File: LICENSE
 Requires-Dist: czifile
 Requires-Dist: Markdown
 Requires-Dist: matplotlib>=3.5.2
-Requires-Dist: numpy
+Requires-Dist: numpy<1.26.4
 Requires-Dist: Pillow>=8.1.2
 Requires-Dist: PyQt6
 Requires-Dist: read-lif
@@ -40,6 +40,8 @@ Requires-Dist: Requests
 Requires-Dist: python-bioformats
 Requires-Dist: python-javabridge
 Requires-Dist: pyautogui
+Requires-Dist: imagecodecs
+Requires-Dist: zarr
 
 # batoolset
 An aggregate of functions I find useful

{batoolset-0.1.0 → batoolset-0.1.2}/batoolset/PATH/tools.py

@@ -47,7 +47,7 @@ def add_epyseg_to_sys_path(file=None, print_only=False):
     else:
         epyseg_path = file
 
-    batoolset_path = __file__.split('epyseg_pkg')[0] + 'batoolset_pkg/'
+    batoolset_path = __file__.split('epyseg_pkg')[0] + 'BAtools_pkg/'
     pyfigures_path = __file__.split('epyseg_pkg')[0] + 'pyfigures_pkg/'
     epyseg_path = __file__.split('epyseg_pkg')[0] + 'epyseg_pkg/'
     dev_path = __file__.split('epyseg_pkg')[0] + 'dev/'

{batoolset-0.1.0 → batoolset-0.1.2}/batoolset/draw/shapes/image2d.py

@@ -311,6 +311,17 @@ class Image2D(Rectangle2D):
             self.px_to_unit_conversion_factor = 0
             # print()
 
+
+    def get_extra_dimensions(self, handle_proj=False):
+        if not isinstance(self.img, np.ndarray):
+            return None
+        guessed_dimensions = guess_dimensions(self.img)
+        extra_dims = guessed_dimensions.replace('h', '').replace('w', '').replace('c', '')
+        if extra_dims and handle_proj:
+            if self.projection is not None:
+                extra_dims = extra_dims[:-1]
+        return extra_dims
+
     def clip_by_frequency(self, lower_cutoff=None, upper_cutoff=0.05, channel_mode=True):
         '''
         Clips the values of an image based on frequency cutoffs.
@@ -463,7 +474,7 @@ class Image2D(Rectangle2D):
         if len(target_dims) > len(image_to_display.shape):
             target_dims = target_dims[len(target_dims)-len(image_to_display.shape):]
 
-        # print('final redndering',image_to_display.shape)
+        # print('final rendering',image_to_display.shape)
         # print('checking img', image_to_display.shape, 'vs', self.img.shape)
         # if self.channels is not None and not self.channels == 'merge' and 'c' in target_dims:
         #         if self.channels>=0 and self.channels < self.img.shape[-1]:
@@ -482,7 +493,6 @@ class Image2D(Rectangle2D):
                 image_to_display = image_to_display[..., np.newaxis]
                 target_dims+='c'
 
-
         if self.channels and 'c' in target_dims:
             # print('inside channels sel self.channels', self.channels)
             list_of_true_indices = bool_list_to_index_list(self.channels)
@@ -646,6 +656,7 @@ class Image2D(Rectangle2D):
         # print('~' * 30)
 
         del image_to_display
+        # del self.img # that would be great but then I would need tricks to know its parameters
 
         # print('----------'*32)
         # return qimage

batoolset-0.1.2/batoolset/images/centralstore.py

@@ -0,0 +1,126 @@
+import os.path
+import traceback
+import gc
+import zarr
+
+# from batoolset.img import Img
+# pb the store should also store metadata  -−> see how I can do that
+
+__DEBUG__ = False
+
+class ImageCentralStore:
+    store = None
+
+    @classmethod
+    def init(cls):
+        cls.store={}
+
+    @classmethod
+    def set_store(cls, store):
+        if __DEBUG__:
+            print('setting store', cls.store)
+        if store:
+            cls.store=store
+        else:
+            cls.store = {}
+
+    @classmethod
+    def get_store(cls):
+        if __DEBUG__:
+            print('getting store', cls.store)
+        return cls.store
+
+    @classmethod
+    def append(cls, image_id, data):
+        # Save the image data to the central store
+        if cls.store is not None:
+            if data is not None:
+                metadata = None
+                if hasattr(data, 'metadata'):
+                    metadata = data.metadata
+                cls.store[image_id] = [metadata,data]
+            else:
+                try:
+                    if __DEBUG__:
+                        print('deleting image store entry because None')
+                    del cls.store[image_id]
+                except:
+                    pass
+            if __DEBUG__:
+                print(f"Image {image_id} added to central store.")
+
+    @classmethod
+    def load(cls, image_id):
+        if False:
+            # shall I do gc
+            # Check if central store is available and if the image exists in the store
+            # gc.collect()
+            # Print the number of objects that were garbage collected
+            print(f"{gc.collect():,} objects were garbage collected")
+        if cls.store is not None:
+            if image_id in cls.store:
+                metadata, img = cls.store[image_id]
+                if __DEBUG__:
+                    print(f"Image {image_id} loaded from central store.")
+                return metadata,img
+            else:
+                metadata, img = cls.reload(image_id)
+                return metadata, img
+
+        if __DEBUG__:
+            print('No store found --> skipping loading from store for', image_id)
+        return None, None
+
+    # maybe put a relaod where the image is necessarily reloaded -−> force an update of the image from source file
+    @classmethod
+    def reload(cls, image_id):
+        from batoolset.img import Img
+        if __DEBUG__:
+            print('Img called for file', image_id)
+        img = Img(image_id,
+                  prefer_store_if_available=False)  # pb will this launch an infinite loop -−> maybe so make sure to prevent reload form it
+        metadata = None
+        if hasattr(img, 'metadata'):
+            metadata = img.metadata
+        # add image to the store
+        cls.append(image_id, img)
+        metadata, data = cls.store[image_id]
+        return metadata, img
+
+    @classmethod
+    def keys(cls):
+        if cls.store:
+            return cls.store.keys()
+        else:
+            return None
+
+    @classmethod
+    def clean_non_existing(cls):
+        keys = cls.keys()
+        if keys:
+            for file in keys:
+                if os.path.exists(file) and os.path.isfile(file):
+                    pass
+                else:
+                    del cls.store[file]
+    @classmethod
+    def clean(cls, sels):
+        cls.clean_non_existing()
+        keys = cls.keys()
+        if keys:
+            # delete entries in cls.store whose keys are not in sels
+            keys_to_delete = set(keys) - set(sels)
+            for key in keys_to_delete:
+                if __DEBUG__:
+                    print('deleting entry from the store', key)
+                del cls.store[key]
+
+        # # add entries in sels that are not in cls.store
+        # keys_to_add = set(sels) - set(cls.store.keys())
+        # for key in keys_to_add:
+        #     cls.store[key] = None  # or some other default value
+
+
+
+
+

{batoolset-0.1.0 → batoolset-0.1.2}/batoolset/img.py

@@ -1,6 +1,7 @@
 from batoolset.tools.logger import TA_logger  # logging
 logger = TA_logger()  # logging_level=TA_logger.DEBUG
 from batoolset.files.tools import smart_name_parser
+from batoolset.images.centralstore import ImageCentralStore
 import random
 import os
 import read_lif  # read Leica .lif files (requires numexpr)
@@ -49,13 +50,15 @@ normalization_ranges = [[0, 1], [-1, 1]]
 def start_JVM():
     # NB BELOW IS MANDATORY TO HAVE SUPPORT FOR BIOFORMATS --> start_JVM SHOULD BE CALLED ONLY ONCE PER INSTANCE AND stop_JVM SHOULD BE CALLED ON LEAVE!
     try:
+        # raise Exception('test error') # force error
         # Start the JVM when the application launches
         import javabridge
         import bioformats
 
         javabridge.start_vm(class_path=bioformats.JARS, run_headless=True, max_heap_size='1G')
     except:
-        pass
+        traceback.print_exc()
+        logger.error('Could not instantiate javabridge bioformats will not work')
 
 def stop_JVM():
     try:
@@ -71,7 +74,8 @@ def guess_dimensions(img):
 
     if hasattr(img, 'metadata'):
         if 'dimensions' in img.metadata:
-            return img.metadata['dimensions']
+            if isinstance(img.metadata['dimensions'],str):
+                return img.metadata['dimensions']
 
     if len(img.shape) == 2:
         return 'hw'
@@ -2824,6 +2828,8 @@ def toQimage(img, autofix_always_display2D=True, normalize=True, z_behaviour=Non
         qimage = QImage(img.data.tobytes(), img.shape[1], img.shape[0], bytesPerLine,
                         QImage.Format_Indexed8)
 
+    del img
+
     return qimage
 
 
@@ -3558,7 +3564,7 @@ class Img(np.ndarray):  # subclass ndarray
     # TODO allow load list of images all specified as strings one by one
     # TODO allow virtual stack --> open only one image at a time from a series, can probably do that with text files
     def __new__(cls, *args, t=0, d=0, z=0, h=0, y=0, w=0, x=0, c=0, bits=8, serie_to_open=None, dimensions=None,
-                metadata=None, **kwargs) -> object:
+                metadata=None, prefer_store_if_available=True, **kwargs) -> object:
         '''Creates a new instance of the Img class
         
         The image class is a numpy ndarray. It is nothing but a matrix of pixel values.
@@ -3628,8 +3634,22 @@ class Img(np.ndarray):  # subclass ndarray
                     # single image
                     creation_time = get_file_creation_time(args[0])
                     try:
+                        # if prefer_store_if_available: # see how I can handle that smartly... -−> not so easy
+
                         try:
-                            meta, img = ImageReader.read(args[0], serie_to_open=serie_to_open)
+                            img = None
+
+                            # print('entering here1')
+
+                            if prefer_store_if_available:
+                                # prefer reload the image from store if available --> will speed up the loading process and spare more resources
+                                # print('entering here2')
+                                meta, img = ImageCentralStore.load(args[0])  # may work
+
+
+                            if img is None:
+                                # print('entering here3')
+                                meta, img = ImageReader.read(args[0], serie_to_open=serie_to_open)
                         except:
                             meta, img = read_file_with_bioformats(args[0])
                     except:
@@ -3669,6 +3689,9 @@ class Img(np.ndarray):  # subclass ndarray
                     img.metadata = meta_data
                     # img.metadata.update({'creation_time': creation_time})
                 else:
+
+                    # TODO --> I need also implement addition of a list to the store -> TODO
+
                     # series of images
                     if isinstance(args[0], list):
                         # the user directly provided a list --> just stack the images -−> can be useful --> there will be error if they don't have same size --> offer options for that but in a later step
@@ -5094,6 +5117,13 @@ class ImageReader:
 
 
 if __name__ == '__main__':
+    if True:
+        from batoolset.tools.logger import TA_logger
+
+
+        print('bob')
+        sys.exit(0)
+
 
     if True:
         # tst = Img('/media/teamPrudhomme/EqpPrudhomme2/Vani/RNAi/Transvection_WT/Het/RNAi_het_20240312/26296_het_F1.tif')

batoolset-0.1.2/batoolset/pyqt/pleasewaitdialog.py

@@ -0,0 +1,14 @@
+from batoolset.settings.global_settings import set_UI # set the UI to qtpy
+set_UI()
+from qtpy.QtWidgets import QApplication, QDialog, QLabel, QVBoxLayout
+
+class PleaseWaitDialog(QDialog):
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setWindowTitle("Please wait")
+        self.setModal(True)
+
+        label = QLabel("Please wait... The slow process is running.")
+        layout = QVBoxLayout()
+        layout.addWidget(label)
+        self.setLayout(layout)

{batoolset-0.1.0 → batoolset-0.1.2}/batoolset/version.py

@@ -1,6 +1,6 @@
 __MAJOR__ = 0
 __MINOR__ = 1
-__MICRO__ = 0
+__MICRO__ = 2
 __RELEASE__ = ''  # a #b  # https://www.python.org/dev/peps/pep-0440/#public-version-identifiers --> alpha beta, ...
 __VERSION__ = ''.join([str(__MAJOR__), '.', str(__MINOR__), '.', str(__MICRO__)])
 __DESCRIPTION__= """An aggregate of functions I find useful"""

batoolset-0.1.2/batoolset/zarr/centralstorezarrstore.py

@@ -0,0 +1,108 @@
+import traceback
+import gc
+import zarr
+
+# from batoolset.img import Img
+# pb the store should also store metadata  -−> see how I can do that
+
+__DEBUG__ = True
+
+class ImageCentralStoreZarr:
+    store = None
+
+    @classmethod
+    def init(cls, folder_path=None):
+        try:
+            if folder_path is None:
+                # Create a Zarr store in memory
+                zarr_store = zarr.MemoryStore()
+            else:
+                zarr_store = zarr.DirectoryStore(folder_path)  # just a single line is sufficient to handle the stuff
+            zarr_root = zarr.group(store=zarr_store)
+            cls.store = zarr_root
+        except:
+            traceback.print_exc()
+            print('Error zarr store could not be created')
+
+    @classmethod
+    def set_store(cls, store):
+        if __DEBUG__:
+            print('setting store', cls.store)
+        # Set the central store (zarr store)
+        if isinstance(store, str):
+            cls.store = zarr.open(store, mode='a')
+        else:
+            cls.store = store
+
+    @classmethod
+    def get_store(cls):
+        if __DEBUG__:
+            print('getting store', cls.store)
+        return cls.store
+
+    @classmethod
+    def append(cls, image_id, data):
+        # Save the image data to the central store
+        if cls.store is not None:
+            if data is not None:
+                cls.store[image_id] = data
+            else:
+                try:
+                    if __DEBUG__:
+                        print('deleting image store entry because None')
+                    del cls.store[image_id]
+                except:
+                    pass
+            if __DEBUG__:
+                print(f"Image {image_id} added to central store.")
+
+            if hasattr(data, 'metadata'):
+                cls.store.attrs[image_id] = data.metadata
+            else:
+                cls.store.attrs[image_id] = None  # just in case there was already a metadata attribute --> make sure to have this
+        # else:
+        #     if __DEBUG__:
+        #         print("Central store is not set.")
+
+    @classmethod
+    def load(cls, image_id):
+        if False:
+            # shall I do gc
+            # Check if central store is available and if the image exists in the store
+            # gc.collect()
+            # Print the number of objects that were garbage collected
+            print(f"{gc.collect():,} objects were garbage collected")
+        if cls.store is not None:
+            if image_id in cls.store:
+                img = cls.store[image_id][:]
+                metadata = cls.store.attrs.get(image_id, None)
+                if __DEBUG__:
+                    print(f"Image {image_id} loaded from central store.")
+                return metadata,img
+            else:
+                metadata, img = cls.reload(image_id)
+                return metadata, img
+
+        if __DEBUG__:
+            print('No store found --> skipping loading from store for', image_id)
+        return None, None
+
+    # maybe put a relaod where the image is necessarily reloaded -−> force an update of the image from source file
+    @classmethod
+    def reload(cls, image_id):
+        from batoolset.img import Img
+        if __DEBUG__:
+            print('Img called for file', image_id)
+        img = Img(image_id,
+                  prefer_store_if_available=False)  # pb will this launch an infinite loop -−> maybe so make sure to prevent reload form it
+        metadata = None
+        if hasattr(img, 'metadata'):
+            metadata = img.metadata
+        # add image to the store
+        cls.append(image_id, img)
+        del img
+
+        img = cls.store[image_id] # then we reload it from the store in order not to duplicate it # MEGA TODO -−> check
+        metadata = cls.store.attrs.get(image_id, None)
+
+        return metadata, img

{batoolset-0.1.0 → batoolset-0.1.2}/batoolset.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: batoolset
-Version: 0.1.0
+Version: 0.1.2
 Summary: An aggregate of functions I find useful
 Home-page: https://github.com/baigouy/batoolset
 Author: Benoit Aigouy
@@ -15,7 +15,7 @@ License-File: LICENSE
 Requires-Dist: czifile
 Requires-Dist: Markdown
 Requires-Dist: matplotlib>=3.5.2
-Requires-Dist: numpy
+Requires-Dist: numpy<1.26.4
 Requires-Dist: Pillow>=8.1.2
 Requires-Dist: PyQt6
 Requires-Dist: read-lif
@@ -40,6 +40,8 @@ Requires-Dist: Requests
 Requires-Dist: python-bioformats
 Requires-Dist: python-javabridge
 Requires-Dist: pyautogui
+Requires-Dist: imagecodecs
+Requires-Dist: zarr
 
 # batoolset
 An aggregate of functions I find useful

{batoolset-0.1.0 → batoolset-0.1.2}/batoolset.egg-info/SOURCES.txt

@@ -80,6 +80,7 @@ batoolset/figure/user_selection.py
 batoolset/files/__init__.py
 batoolset/files/tools.py
 batoolset/images/__init__.py
+batoolset/images/centralstore.py
 batoolset/images/tools.py
 batoolset/linux/__init__.py
 batoolset/linux/tools.py
@@ -99,6 +100,7 @@ batoolset/partials/tools.py
 batoolset/plot_tools/__init__.py
 batoolset/plot_tools/tools.py
 batoolset/pyqt/__init__.py
+batoolset/pyqt/pleasewaitdialog.py
 batoolset/pyqt/tools.py
 batoolset/re_tools/__init__.py
 batoolset/re_tools/tools.py
@@ -161,5 +163,7 @@ batoolset/utils/commontools.py
 batoolset/utils/loadlist.py
 batoolset/xml/__init__.py
 batoolset/xml/tools.py
+batoolset/zarr/__init__.py
+batoolset/zarr/centralstorezarrstore.py
 batoolset/zip_tools/__init__.py
 batoolset/zip_tools/tools.py

{batoolset-0.1.0 → batoolset-0.1.2}/batoolset.egg-info/requires.txt

@@ -1,7 +1,7 @@
 czifile
 Markdown
 matplotlib>=3.5.2
-numpy
+numpy<1.26.4
 Pillow>=8.1.2
 PyQt6
 read-lif
@@ -26,3 +26,5 @@ Requests
 python-bioformats
 python-javabridge
 pyautogui
+imagecodecs
+zarr

{batoolset-0.1.0 → batoolset-0.1.2}/setup.py

@@ -26,7 +26,7 @@ setuptools.setup(
         "czifile",
         "Markdown",
         "matplotlib>=3.5.2",
-        "numpy",
+        "numpy<1.26.4", # <1.26.4 for compat with javabridge
         "Pillow>=8.1.2",
         "PyQt6",
         "read-lif",
@@ -51,6 +51,8 @@ setuptools.setup(
         "python-bioformats",
         "python-javabridge",
         "pyautogui",
+        "imagecodecs",
+        "zarr",
     ],
     python_requires='>=3.7, <3.11' # from 04/05/23 colab is using python 3.10.11
 )