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ENH: Update image table - allow for labels for images/scenes
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@aylward
aylward committed Aug 4, 2024
1 parent e922521 commit 85a8da9
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Showing 6 changed files with 105 additions and 29 deletions.
2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ For windows running gitbash

Install the test-build of ITK, ITKMinimalPathExtraction ITKTubetk:

python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ itk itk-minimalpathextraction itk-tubetk
python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ --upgrade itk itk-minimalpathextraction itk-tubetk

Get the Minder3D source code

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70 changes: 55 additions & 15 deletions src/minder3d/lib/sovImageTablePanelWidget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,20 +42,21 @@ def __init__(self, gui, state, parent=None):
self.selected_icon = self.style().standardIcon(pixmapi)

self.imageTableWidget.setRowCount(0)
self.imageTableWidget.setColumnCount(7)
self.imageTableWidget.setColumnCount(8)
self.imageTableWidget.setHorizontalHeaderLabels(
[
'Selected',
'Loaded',
'Type',
'Thumbnail',
'Label',
'Size',
'Spacing',
'Filename',
]
)
self.col_filetype = 2
self.col_filename = 6
self.col_filename = 7
self.imageTableWidget.setEditTriggers(QTableWidget.NoEditTriggers)
self.imageTableWidget.setSelectionBehavior(QTableWidget.SelectRows)
self.imageTableWidget.setSelectionMode(QTableWidget.SingleSelection)
Expand Down Expand Up @@ -96,40 +97,46 @@ def unload_selected(self):
self.selected = []
self.fill_table()

@time_and_log
def remove_selected(self):
for row in self.selected:
if row < len(self.state.image_filename):
self.gui.unload_image(row, False)
self.settings.remove_data(self.state.image_filename[row])
elif row == len(self.state.image_filename):
elif (
row == len(self.state.image_filename)
and self.state.scene_filename
!= self.imageTableWidget.item(row, self.col_filename).text()
):
self.gui.unload_scene()
self.settings.remove_data(self.state.scene_filename)
self.settings.remove_data(self.state.image_filename[row])
else:
filename = str(
self.imageTableWidget.getItem(
row, self.col_filename
).values[0]
self.settings.remove_data(
self.imageTableWidget.item(row, self.col_filename).text()
)
self.settings.remove_data(filename)
if len(self.selected) > 0:
self.selected = []
self.fill_table()

@time_and_log
def remove_all(self):
num_images = len(self.state.image_filename)
for row in range(num_images - 1, 0, -1):
self.gui.unload_image(row, False)
self.settings.remove_data(self.state.image_filename[row])
self.gui.unload_scene()
self.settings.remove_data(self.state.scene_filename)
for row in range(self.imageTableWidget.getRowCount()):
if row < num_images:
self.gui.unload_image(row, False)
self.settings.remove_data(
self.imageTableWidget.item(row, self.col_filename).text()
)
self.selected = []
self.settings.clear_data()
self.fill_table()

@time_and_log
def close_expanded_table(self):
self.enlarged_table.close()
self.enlarged_table = None

@time_and_log
def expand_table(self):
if self.enlarged_table is None:
self.enlarged_table = ImageTablePanelWidget(self.gui, self.state)
Expand Down Expand Up @@ -204,6 +211,12 @@ def redraw_image_row(self, row_num):
QTableWidgetItem(QIcon(self.state.image_thumbnail[img_num]), ''),
)
col_num += 1
self.imageTableWidget.setItem(
row_num,
col_num,
QTableWidgetItem(QIcon(self.state.image_label[img_num]), ''),
)
col_num += 1
size_str = [
str(i)
for i in self.state.image[img_num]
Expand Down Expand Up @@ -261,6 +274,10 @@ def redraw_scene_row(self, row_num):
QTableWidgetItem(QIcon(self.state.scene_thumbnail), ''),
)
col_num += 1
self.imageTableWidget.setItem(
row_num, col_num, QTableWidgetItem(self.state.scene_label)
)
col_num += 1
size = self.state.scene.GetNumberOfChildren()
self.imageTableWidget.setItem(
row_num, col_num, QTableWidgetItem(str(size))
Expand Down Expand Up @@ -296,6 +313,7 @@ def fill_table(self):
'Loaded',
'Type',
'Thumbnail',
'Label',
'Size',
'Spacing',
'Filename',
Expand Down Expand Up @@ -349,6 +367,10 @@ def fill_table(self):
row_num, col_num, QTableWidgetItem(' ')
)
col_num += 1
self.imageTableWidget.setItem(
row_num, col_num, QTableWidgetItem(str(file.file_label))
)
col_num += 1
self.imageTableWidget.setItem(
row_num, col_num, QTableWidgetItem(str(file.file_size))
)
Expand Down Expand Up @@ -392,6 +414,10 @@ def fill_table(self):
row_num, col_num, QTableWidgetItem(QIcon(qthumb), '')
)
col_num += 1
self.imageTableWidget.setItem(
row_num, col_num, QTableWidgetItem(file.file_label)
)
col_num += 1
self.imageTableWidget.setItem(
row_num, col_num, QTableWidgetItem(file.file_size)
)
Expand All @@ -407,6 +433,9 @@ def fill_table(self):

@time_and_log
def create_new_image(self):
self.state.image_label.append(
os.path.basename(self.state.image_filename[-1])
)
self.state.image_thumbnail.append(
self.settings.get_thumbnail(
self.state.image[-1], self.state.image_filename[-1], 'image'
Expand All @@ -416,6 +445,7 @@ def create_new_image(self):
self.state.image[-1],
self.state.image_filename[-1],
'image',
self.state.image_label[-1],
self.state.image_thumbnail[-1],
)
self.selected = []
Expand All @@ -427,6 +457,7 @@ def save_image(self, filename):
self.state.image[self.state.current_image_num],
filename,
'image',
self.state.image_label[self.state.current_image_num],
self.state.image_thumbnail[self.state.current_image_num],
)
self.selected = []
Expand All @@ -437,10 +468,12 @@ def load_scene(self):
self.state.scene_thumbnail = self.settings.get_thumbnail(
self.state.scene, self.state.scene_filename, 'scene'
)
self.state.scene_label = os.path.basename(self.state.scene_filename)
self.settings.add_data(
self.state.scene,
self.state.scene_filename,
'scene',
self.state.scene_label,
self.state.scene_thumbnail,
)
self.selected = []
Expand All @@ -449,13 +482,18 @@ def load_scene(self):
@time_and_log
def save_scene(self, filename):
self.settings.add_data(
self.state.scene, filename, 'scene', self.state.scene_thumbnail
self.state.scene,
filename,
'scene',
self.state.scene_label,
self.state.scene_thumbnail,
)

@time_and_log
def replace_image(self, img_num):
self.redraw_image_row(img_num)

@time_and_log
def rename_selected(self):
pass

Expand Down Expand Up @@ -521,12 +559,14 @@ def register_images(self, dir, first=True):
img = imread(filename)
except Exception:
continue
label = os.path.basename(filename)
thumbnail = self.settings.get_thumbnail(img, filename, 'image')
print(f'Adding {filename} to settings')
self.settings.add_data(
img,
filename,
'image',
label,
thumbnail,
)

Expand Down
25 changes: 22 additions & 3 deletions src/minder3d/lib/sovImageTableSettings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ def __init__(
file_spacing='',
file_size='',
file_thumbnail='',
file_label='',
):
"""Initialize the object with the provided file details.
Expand All @@ -26,13 +27,15 @@ def __init__(
file_spacing (str): A list of spacing details. Defaults to ''.
file_size (str): A list of size details. Defaults to ''.
file_thumbnail (str): The thumbnail of the file. Defaults to ''.
file_label (str): The short diaplay-name of the file. Defaults to ''.
"""

self.filename = filename
self.file_type = file_type
self.file_spacing = file_spacing
self.file_size = file_size
self.file_thumbnail = file_thumbnail
self.file_label = file_label


class ImageTableSettings(QSettings):
Expand Down Expand Up @@ -69,15 +72,23 @@ def get_file_records(self):
file_spacing = self.value('file_spacing', '')
file_size = self.value('file_size', '')
file_thumbnail = self.value('file_thumbnail', '')
file_label = self.value('file_label', '')
file = ImageTableSettingsFileRecord(
filename, file_type, file_spacing, file_size, file_thumbnail
filename,
file_type,
file_spacing,
file_size,
file_thumbnail,
file_label,
)
file_records.append(file)
self.endArray()
return file_records

@time_and_log
def add_data(self, obj, filename, file_type, thumbnail_pixmap=None):
def add_data(
self, obj, filename, file_type, file_label=None, thumbnail_pixmap=None
):
"""Add a file to the settings.
This function adds a file to the settings, including its filename, type,
Expand All @@ -87,6 +98,7 @@ def add_data(self, obj, filename, file_type, thumbnail_pixmap=None):
obj: The object representing the file.
filename (str): The name of the file.
file_type (str): The type of the file.
file_label (Optional[str]): The custom label of file, defaults to basename of filename
thumbnail_pixmap (Optional[QPixmap]): The thumbnail of the file.
Expand Down Expand Up @@ -115,6 +127,8 @@ def add_data(self, obj, filename, file_type, thumbnail_pixmap=None):
file_thumbnail = os.path.join(data_dir, file_thumbnail)
if not thumbnail_pixmap.save(file_thumbnail):
file_thumbnail = ''
if file_label is None or file_label == '':
file_label = os.path.basename(filename)

self.beginWriteArray('files')
for i, file in enumerate(file_records):
Expand All @@ -128,6 +142,7 @@ def add_data(self, obj, filename, file_type, thumbnail_pixmap=None):
):
os.remove(file.file_thumbnail)
self.setValue('file_thumbnail', file_thumbnail)
self.setValue('file_label', file_label)
self.setArrayIndex(len(file_records) - 1)
self.endArray()
self.sync()
Expand All @@ -145,12 +160,14 @@ def add_data(self, obj, filename, file_type, thumbnail_pixmap=None):
self.setValue('file_spacing', file.file_spacing)
self.setValue('file_size', file.file_size)
self.setValue('file_thumbnail', file.file_thumbnail)
self.setValue('file_label', file.file_label)
self.setArrayIndex(len(file_records))
self.setValue('filename', filename)
self.setValue('file_type', file_type)
self.setValue('file_spacing', file_spacing)
self.setValue('file_size', file_size)
self.setValue('file_thumbnail', file_thumbnail)
self.setValue('file_label', file_label)
self.setArrayIndex(len(file_records) - 1)
self.endArray()
self.sync()
Expand Down Expand Up @@ -182,11 +199,12 @@ def remove_data(self, filename):
for j in range(i + 1, len(file_records)):
next_file = file_records[j]
self.setArrayIndex(j - 1)
self.setValue('file_filename', next_file.file_filename)
self.setValue('file_filename', next_file.filename)
self.setValue('file_type', next_file.file_type)
self.setValue('file_spacing', next_file.file_spacing)
self.setValue('file_size', next_file.file_size)
self.setValue('file_thumbnail', next_file.file_thumbnail)
self.setValue('file_label', next_file.file_label)
self.sync()
return
else:
Expand All @@ -196,6 +214,7 @@ def remove_data(self, filename):
self.setValue('file_spacing', next_file.file_spacing)
self.setValue('file_size', next_file.file_size)
self.setValue('file_thumbnail', next_file.file_thumbnail)
self.setValue('file_label', next_file.file_label)
self.sync()
return

Expand Down
15 changes: 5 additions & 10 deletions src/minder3d/lib/sovImportDICOMSettings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,18 +18,13 @@ def __init__(self):
def add_data(self, input_directory, output_directory, auto_register):
"""Add a data settings.
This function adds a file to the settings, including its filename, type,
spacing, size, and thumbnail.
This function converts a DICOM directory of files to .nii.gz files.
Optionally adds them to the settings database.
Args:
obj: The object representing the file.
filename (str): The name of the file.
file_type (str): The type of the file.
thumbnail_pixmap (Optional[QPixmap]): The thumbnail of the file.
Raises:
IndexError: If the input list is empty.
input_directory (str): The directory containing DICOM data.
output_directory (str): The directory for storing the nii.gz files.
auto_register (Optional[bool]): Should the created nii.gz files be stored in the settings database.
"""
self.setValue('input_directory', input_directory)
self.setValue('output_directory', output_directory)
Expand Down
2 changes: 2 additions & 0 deletions src/minder3d/minder3DState.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ def __init__(self):
self.image_max = []
self.image_filename = []
self.image_thumbnail = []
self.image_label = []
self.csa_to_image_axis = []

# Overlay
Expand Down Expand Up @@ -63,6 +64,7 @@ def __init__(self):
self.scene_list_properties = dict()
self.scene_filename = './scene.tre'
self.scene_thumbnail = None
self.scene_label = None

# Selected Spatial Objects
self.multiple_selections_enabled = False
Expand Down
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