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napari fileselect docs
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@aelefebv
aelefebv committed Oct 3, 2024
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169 changes: 169 additions & 0 deletions nellie_napari/nellie_fileselect.py
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Expand Up @@ -9,7 +9,100 @@


class NellieFileSelect(QWidget):
"""
A class for selecting and configuring image files for processing in the Nellie pipeline within the napari viewer.
Attributes
----------
viewer : napari.viewer.Viewer
The napari viewer instance.
nellie : object
Reference to the main Nellie object containing image processing pipelines and functions.
filepath : str or None
The selected file path.
file_info : FileInfo
Stores metadata and shape information about the selected image file.
im_info : ImInfo or None
Contains information about the image for processing after confirmation.
batch_fileinfo_list : list or None
List of FileInfo objects when a folder is selected for batch processing.
filepath_text : QLabel
Text widget displaying the selected file or folder path.
filepath_button : QPushButton
Button to open the file dialog for selecting an image file.
folder_button : QPushButton
Button to open the folder dialog for batch processing.
reset_button : QPushButton
Button to reset the file selection and clear all settings.
file_shape_text : QLabel
Displays the shape of the selected image file.
current_order_text : QLabel
Displays the current dimension order (axes) of the image file.
dim_order_button : QLineEdit
Input field for entering the dimension order of the image.
dim_t_button, dim_z_button, dim_xy_button : QLineEdit
Input fields for entering the resolution of the time (T), Z, and XY dimensions, respectively.
channel_button : QSpinBox
Spin box for selecting the channel in the multi-channel image.
start_frame_button, end_frame_button : QSpinBox
Spin boxes for selecting the start and end frame for temporal range selection.
confirm_button : QPushButton
Button to confirm the file selection and save the OME TIFF file.
preview_button : QPushButton
Button to preview the image in the napari viewer.
process_button : QPushButton
Button to process the selected image file(s) through the Nellie pipeline.
Methods
-------
init_ui()
Sets up the user interface layout with file selection, axes information, dimension resolutions, and actions.
select_filepath()
Opens a file dialog for selecting an image file and validates the selected file.
select_folder()
Opens a folder dialog for batch processing and validates the selected folder.
validate_path(filepath)
Validates the selected file or folder path and updates the file path attribute.
initialize_single_file()
Initializes the FileInfo for the selected image file, loads metadata, and updates UI elements.
initialize_folder()
Initializes the FileInfo objects for all image files in the selected folder.
on_change()
Updates UI elements based on the selected file's metadata, checking available dimensions and enabling buttons.
check_available_dims()
Checks the availability of specific dimensions (T, Z, XY) in the selected file and enables corresponding UI elements.
handle_dim_order_changed(text)
Handles changes in the dimension order (axes) input field and updates the metadata accordingly.
handle_t_changed(text)
Handles changes in the time (T) resolution input field and updates the metadata.
handle_z_changed(text)
Handles changes in the Z resolution input field and updates the metadata.
handle_xy_changed(text)
Handles changes in the XY resolution input field and updates the metadata.
change_channel()
Updates the selected channel for the image when the channel spin box is changed.
change_time()
Updates the temporal range when the start and end frame spin boxes are changed.
on_confirm()
Confirms the file selection, creates an ImInfo object, and prepares the file for processing.
on_process()
Prepares the selected file(s) for processing through the Nellie pipeline.
on_preview()
Opens a preview of the selected image in the napari viewer, adjusting the display settings based on the file's dimensionality.
"""
def __init__(self, napari_viewer: 'napari.viewer.Viewer', nellie, parent=None):
"""
Initializes the NellieFileSelect class.
Parameters
----------
napari_viewer : napari.viewer.Viewer
Reference to the napari viewer instance.
nellie : object
Reference to the main Nellie object containing image processing pipelines and functions.
parent : QWidget, optional
Optional parent widget (default is None).
"""
super().__init__(parent)
self.nellie = nellie
self.filepath = None
Expand Down Expand Up @@ -113,6 +206,9 @@ def __init__(self, napari_viewer: 'napari.viewer.Viewer', nellie, parent=None):
self.init_ui()

def init_ui(self):
"""
Sets up the user interface layout with sections for file selection, axes information, dimension resolutions, and action buttons.
"""
main_layout = QVBoxLayout()

# File Selection Group
Expand Down Expand Up @@ -193,6 +289,9 @@ def init_ui(self):
self.setLayout(main_layout)

def select_filepath(self):
"""
Opens a file dialog for selecting an image file, validates the selected file, and updates the UI with metadata.
"""
self.batch_fileinfo_list = None
filepath, _ = QFileDialog.getOpenFileName(self, "Select file")
self.validate_path(filepath)
Expand All @@ -206,6 +305,9 @@ def select_filepath(self):
self.filepath_text.setText(f"{filename}")

def select_folder(self):
"""
Opens a folder dialog for selecting a folder for batch processing and initializes FileInfo objects for all files in the folder.
"""
folderpath = QFileDialog.getExistingDirectory(self, "Select folder")
self.validate_path(folderpath)
if self.filepath is None:
Expand All @@ -217,12 +319,23 @@ def select_folder(self):


def validate_path(self, filepath):
"""
Validates the selected file or folder path and updates the file path attribute.
Parameters
----------
filepath : str
The file or folder path selected by the user.
"""
if not filepath:
show_info("Invalid selection.")
return None
self.filepath = filepath

def initialize_single_file(self):
"""
Initializes the FileInfo object for the selected image file, loads metadata, and updates the dimension resolution fields.
"""
self.file_info.find_metadata()
self.file_info.load_metadata()
self.file_shape_text.setText(f"{self.file_info.shape}")
Expand All @@ -232,6 +345,9 @@ def initialize_single_file(self):
self.on_change()

def initialize_folder(self):
"""
Initializes FileInfo objects for all .tif, .tiff, and .nd2 files in the selected folder and loads their metadata.
"""
# get all .tif, .tiff, and .nd2 files in the folder
files = [f for f in os.listdir(self.filepath) if f.endswith('.tif') or f.endswith('.tiff') or f.endswith('.nd2')]
# for each file, create a FileInfo object
Expand All @@ -244,6 +360,9 @@ def initialize_folder(self):
# This assumes all files in the folder have the same metadata (dim order, resolutions, temporal range, channels)

def on_change(self):
"""
Updates the user interface elements, including enabling or disabling buttons based on the file metadata and resolution settings.
"""
self.confirm_button.setEnabled(False)
self.check_available_dims()
if len(self.file_info.shape) == 2:
Expand Down Expand Up @@ -279,6 +398,9 @@ def on_change(self):
self.process_button.setEnabled(True)

def check_available_dims(self):
"""
Checks the availability of specific dimensions (T, Z, XY) in the selected file and enables the corresponding input fields for resolutions.
"""
def check_dim(dim, dim_button, dim_text):
dim_button.setStyleSheet("background-color: green")
if dim in self.file_info.axes:
Expand Down Expand Up @@ -324,6 +446,14 @@ def check_dim(dim, dim_button, dim_text):
self.end_frame_init = True

def handle_dim_order_changed(self, text):
"""
Handles changes in the dimension order input field and updates the FileInfo object accordingly.
Parameters
----------
text : str
The new dimension order string entered by the user.
"""
if self.batch_fileinfo_list is None:
self.file_info.change_axes(text)
else:
Expand All @@ -334,6 +464,14 @@ def handle_dim_order_changed(self, text):
self.on_change()

def handle_t_changed(self, text):
"""
Handles changes in the time (T) resolution input field and updates the FileInfo object accordingly.
Parameters
----------
text : str
The new T resolution entered by the user.
"""
self.dim_t_text = text
try:
value = float(self.dim_t_text)
Expand All @@ -351,6 +489,14 @@ def handle_t_changed(self, text):
self.on_change()

def handle_z_changed(self, text):
"""
Handles changes in the Z resolution input field and updates the FileInfo object accordingly.
Parameters
----------
text : str
The new Z resolution entered by the user.
"""
self.dim_z_text = text
try:
value = float(self.dim_z_text)
Expand All @@ -368,6 +514,14 @@ def handle_z_changed(self, text):
self.on_change()

def handle_xy_changed(self, text):
"""
Handles changes in the XY resolution input field and updates the FileInfo object accordingly.
Parameters
----------
text : str
The new XY resolution entered by the user.
"""
self.dim_xy_text = text
try:
value = float(self.dim_xy_text)
Expand All @@ -389,6 +543,9 @@ def handle_xy_changed(self, text):
self.on_change()

def change_channel(self):
"""
Updates the selected channel in the FileInfo object when the channel spin box value is changed.
"""
if self.batch_fileinfo_list is None:
self.file_info.change_selected_channel(self.channel_button.value())
else:
Expand All @@ -397,6 +554,9 @@ def change_channel(self):
self.on_change()

def change_time(self):
"""
Updates the temporal range in the FileInfo object when the start or end frame spin box values are changed.
"""
if self.batch_fileinfo_list is None:
self.file_info.select_temporal_range(self.start_frame_button.value(), self.end_frame_button.value())
else:
Expand All @@ -405,6 +565,9 @@ def change_time(self):
self.on_change()

def on_confirm(self):
"""
Confirms the file selection, creates an ImInfo object for the file, and prepares it for processing.
"""
show_info("Saving OME TIFF file.")
if self.batch_fileinfo_list is None:
self.im_info = ImInfo(self.file_info)
Expand All @@ -413,6 +576,9 @@ def on_confirm(self):
self.on_change()

def on_process(self):
"""
Prepares the selected file(s) for processing through the Nellie pipeline by creating ImInfo objects and switching to the processing tab.
"""
# switch to process tab
if self.batch_fileinfo_list is None:
self.im_info = ImInfo(self.file_info)
Expand All @@ -422,6 +588,9 @@ def on_process(self):
self.nellie.go_process()

def on_preview(self):
"""
Opens a preview of the selected image in the napari viewer, adjusting display settings (e.g., 2D or 3D view) based on the file's dimensionality.
"""
im_memmap = tifffile.memmap(self.file_info.ome_output_path)
# num_t = min(2, self.im_info.shape[self.im_info.axes.index('T')])
if 'Z' in self.file_info.axes:
Expand Down

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