- First real commit.
This commit is contained in:
Wim Pomp
@@ -1,2 +1,2 @@
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# tiffexplore
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# TIFF Explorer
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Explore tiff structures, tags, and frames in a GUI.
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6
bin/tiffexplore
Normal file
6
bin/tiffexplore
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@@ -0,0 +1,6 @@
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#!/usr/bin/env python3
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from tiffexplore import main
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if __name__ == '__main__':
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main()
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23
setup.py
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23
setup.py
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@@ -0,0 +1,23 @@
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import setuptools
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with open("README.md", "r") as fh:
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long_description = fh.read()
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setuptools.setup(
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name="tiffexplore",
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packages=["tiffexplore"],
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version="2021.06.0",
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author="Wim Pomp",
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author_email="wimpomp@gmail.com",
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description="Explore a tiff structure.",
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long_description=long_description,
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long_description_content_type="text/markdown",
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classifiers=[
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"Programming Language :: Python :: 3",
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"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
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"Operating System :: OS Independent",
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],
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python_requires='>=3.7',
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install_requires=['numpy', 'tifffile', 'PyQt5'],
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scripts=['bin/tiffexplore'],
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)
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246
tiffexplore/__init__.py
Normal file
246
tiffexplore/__init__.py
Normal file
@@ -0,0 +1,246 @@
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#!/usr/bin/env python3
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from PyQt5 import QtCore, QtWidgets, QtGui
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from os.path import isfile, basename
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from sys import argv
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if __package__ is None:
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import tiffread
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else:
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from . import tiffread
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class UiMainWindow(object):
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def setupUi(self, MainWindow):
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MainWindow.resize(800, 600)
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self.centralwidget = QtWidgets.QWidget(MainWindow)
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self.centrallayout = QtWidgets.QHBoxLayout(self.centralwidget)
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self.scrollArea = QtWidgets.QScrollArea(self.centralwidget)
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self.scrollArea.setFixedWidth(150)
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self.scrollArea.setMinimumHeight(200)
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self.scrollArea.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)
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self.scrollArea.setWidgetResizable(True)
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self.leftcolumnWidget = QtWidgets.QWidget()
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self.leftcolumnWidget.setFixedWidth(130)
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self.leftcolumnWidget.setMinimumHeight(200)
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self.verticalLayoutWidget = QtWidgets.QWidget(self.leftcolumnWidget)
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self.verticalLayoutWidget.setFixedWidth(130)
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self.verticalLayoutWidget.setMinimumHeight(200)
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self.leftcolumn = QtWidgets.QVBoxLayout(self.verticalLayoutWidget)
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self.leftcolumn.setContentsMargins(0, 0, 0, 0)
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self.scrollArea.setWidget(self.leftcolumnWidget)
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self.middlecolumnWidget = QtWidgets.QWidget()
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self.middlecolumn = QtWidgets.QVBoxLayout(self.middlecolumnWidget)
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self.middlecolumn.setContentsMargins(0, 0, 0, 0)
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self.properties = QtWidgets.QTextEdit(self.centralwidget)
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self.middlecolumn.addWidget(self.properties)
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self.rightcolumnWidget = QtWidgets.QWidget()
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self.rightcolumn = QtWidgets.QVBoxLayout(self.rightcolumnWidget)
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self.rightcolumn.setContentsMargins(0, 0, 0, 0)
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self.binary = QtWidgets.QTextEdit(self.rightcolumnWidget)
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self.rightcolumn.addWidget(self.binary)
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self.image = QtWidgets.QLabel(self.rightcolumnWidget)
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self.image.setMinimumWidth(200)
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self.image.setMinimumHeight(200)
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self.rightcolumn.addWidget(self.image)
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MainWindow.setCentralWidget(self.centralwidget)
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self.menubar = QtWidgets.QMenuBar(MainWindow)
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self.menubar.setGeometry(QtCore.QRect(0, 0, 800, 22))
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self.menubar.setObjectName("menubar")
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self.menuFile = QtWidgets.QMenu(self.menubar)
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self.menuFile.setObjectName("menuFile")
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MainWindow.setMenuBar(self.menubar)
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self.statusbar = QtWidgets.QStatusBar(MainWindow)
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self.statusbar.setObjectName("statusbar")
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MainWindow.setStatusBar(self.statusbar)
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self.actionOpen = QtWidgets.QAction(MainWindow)
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self.actionOpen.setObjectName("actionOpen")
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self.menuFile.addAction(self.actionOpen)
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self.menubar.addAction(self.menuFile.menuAction())
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self.centrallayout.addWidget(self.scrollArea)
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self.centrallayout.addWidget(self.middlecolumnWidget)
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self.centrallayout.addWidget(self.rightcolumnWidget)
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self.centralwidget.setLayout(self.centrallayout)
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self.retranslateUi(MainWindow)
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QtCore.QMetaObject.connectSlotsByName(MainWindow)
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def retranslateUi(self, MainWindow):
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_translate = QtCore.QCoreApplication.translate
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MainWindow.setWindowTitle(_translate("MainWindow", "TiffExp"))
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self.menuFile.setTitle(_translate("MainWindow", "File"))
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self.actionOpen.setText(_translate("MainWindow", "Open"))
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self.actionOpen.setShortcut(_translate("MainWindow", "Ctrl+O"))
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class PaintBox(QtWidgets.QWidget):
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def drawText(self, qp, rect, text):
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qp.setPen(QtGui.QColor('black'))
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qp.setFont(QtGui.QFont('Decorative', 10 if rect[3] > 20 else rect[3] // 2))
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qp.drawText(QtCore.QRect(*rect), QtCore.Qt.AlignCenter, text)
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def drawRectangle(self, qp, rect, color):
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color = QtGui.QColor(color) if isinstance(color, str) else QtGui.QColor(*color)
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qp.setPen(QtGui.QColor('gray'))
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qp.setBrush(color)
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qp.drawRect(*rect)
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class Legend(PaintBox):
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def __init__(self, parent):
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self.parent = parent
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self.color = {'header': 'red', 'ifd': 'cyan', 'tagdata': 'lightgreen', 'image': 'yellow', 'empty': 'white',
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'shared tagdata': 'green', 'shared image': 'orange', 'unknown': 'gray'}
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super().__init__()
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self.setFixedHeight(120)
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self.show()
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def paintEvent(self, *args, **kwargs):
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qp = QtGui.QPainter()
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qp.begin(self)
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for i, (key, value) in enumerate(self.color.items()):
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self.drawRectangle(qp, (0, 15*i, 125, 15), value)
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self.drawText(qp, (0, 15*i, 125, 15), key)
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qp.end()
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class Bar(PaintBox):
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def __init__(self, parent):
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self.parent = parent
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self.color = {'header': 'red', 'ifd': 'cyan', 'tagdata': 'lightgreen', 'image': 'yellow', 'empty': 'white',
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'HEADER': 'red', 'IFD': 'blue', 'TAGDATA': 'green', 'IMAGE': 'orange', 'EMPTY': 'white'}
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self.tiff = None
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self.bar = tiffread.assignments()
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super().__init__()
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self.setFixedWidth(150)
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self.show()
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def new_file(self):
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self.tiff = self.parent.tiff
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self.bar = tiffread.assignments() if self.tiff is None else self.get_bar()
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self.parent.leftcolumnWidget.setFixedHeight(self.bar.max_addr)
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self.parent.verticalLayoutWidget.setFixedHeight(self.bar.max_addr)
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def paintEvent(self, *args, **kwargs):
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qp = QtGui.QPainter()
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qp.begin(self)
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self.parent.leftcolumnWidget.setFixedHeight(self.bar.max_addr)
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self.parent.verticalLayoutWidget.setFixedHeight(self.bar.max_addr)
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for key, value in self.bar.items():
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self.drawRectangle(qp, (0, value[0], 125, value[1]), self.color.get(key[0], "gray"))
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self.drawText(qp, (0, value[0], 125, value[1]), ('_'.join(('{}',) * len(key))).format(*key).lower())
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qp.end()
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def get_bar(self):
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min_size = 10
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scale = 100
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bar = tiffread.assignments()
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pos = 0
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for item in self.tiff.addresses.get_assignments():
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key, value = item[0]
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size = value[1] // scale if value[1] // scale >= min_size else min_size
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if not (key[0].lower() == 'empty' and value[1] == 1):
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if key[0].lower() == 'empty':
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bar[('empty', value[0] + value[1] // 2)] = (pos, size)
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else:
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if len(item) > 1:
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bar[(key[0].upper(),) + key[1:]] = (pos, size)
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else:
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bar[key] = (pos, size)
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pos += size
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bar.max_addr = pos
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return bar
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def mousePressEvent(self, event):
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keys, vals = zip(*self.bar.get_assignment(event.localPos().y()))
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key, val = keys[0], vals[0]
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if key[0].lower() == 'empty':
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addr = key[1]
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else:
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addr = self.tiff.addresses[(key[0].lower(),) + key[1:]]
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addr = addr[0] + addr[1] // 2
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keys, addrs = zip(*self.parent.tiff.addresses.get_assignment(addr))
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addr = addrs[0]
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text = [('_'.join(('{}',) * len(key))).format(*key) for key in keys]
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text.append('')
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text.append(f'Adresses: {addr[0]} - {sum(addr)}')
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text.append(f'Length: {addr[1]}')
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text.append('')
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if key[0].lower() == 'header':
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text.append(f'File size: {len(self.tiff)}')
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text.append(f'Byte order: {self.tiff.byteorder}')
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text.append(f'Big tiff: {self.tiff.bigtiff}')
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text.append(f'Tag size: {self.tiff.tagsize}')
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text.append(f'Tag number format: {self.tiff.tagnoformat}')
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text.append(f'Offset size: {self.tiff.offsetsize}')
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text.append(f'Offset format: {self.tiff.offsetformat}')
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text.append(f'First ifd offset: {self.tiff.offset}')
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if key[0].lower() == 'ifd':
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text.extend([f'{k}: {v}' for k, v in self.tiff.tags[key[1]].items()])
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if key[1] < self.tiff.nifds-1:
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text.append(f'Next ifd offset: {self.tiff.addresses[("ifd", key[1] + 1)][0]}')
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if key[0].lower() == 'tagdata':
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text.append(f'{key[2]}: {self.tiff.tags[key[1]][key[2]]}')
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if key[0].lower() == 'image':
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self.parent.setImage(key[1], key[2])
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else:
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self.parent.setImage()
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self.parent.properties.setText('\n'.join(text))
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self.parent.binary.setText(''.join([chr(i) for i in self.tiff[addr[0]:addr[0]+addr[1]]]))
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class App(QtWidgets.QMainWindow, UiMainWindow):
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def __init__(self, tiff=None):
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super().__init__()
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self.tiff = None
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self.setupUi(self)
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self.bar = Bar(self)
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self.leftcolumn.addWidget(self.bar)
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self.legend = Legend(self)
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self.middlecolumn.addWidget(self.legend)
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self.actionOpen.triggered.connect(self.openDialog)
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self.open(tiff)
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self.show()
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def setImage(self, *args):
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if len(args):
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im = self.tiff.asarray(*args)
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if im.ndim == 3:
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im = im[0]
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if im.max() - im.min() > 0:
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im = (255 * ((im - im.min()) / (im.max() - im.min()))).astype('uint8')
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shape = im.shape
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im = QtGui.QImage(im, im.shape[1], im.shape[0], QtGui.QImage.Format_Grayscale8)
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f = min([a / b for a, b in zip((self.image.height(), self.image.width()), shape)])
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pix = QtGui.QPixmap(im).scaled(f * shape[1], f * shape[0])
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else:
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pix = QtGui.QPixmap()
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self.image.setPixmap(pix)
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def openDialog(self):
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file, _ = QtWidgets.QFileDialog.getOpenFileName(self,
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"Open config file", "", "TIFF Files (*.tif *.tiff);;All Files (*)",
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options=(QtWidgets.QFileDialog.Options() | QtWidgets.QFileDialog.DontUseNativeDialog))
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self.open(file)
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def open(self, file):
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if file is not None and isfile(file):
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if self.tiff is not None:
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self.tiff.close()
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self.tiff = tiffread.tiff(file)
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self.bar.new_file()
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self.setWindowTitle(f'TiffExp: {basename(self.tiff.file)}')
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def closeEvent(self, *args, **kwargs):
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if self.tiff is not None:
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self.tiff.close()
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def main():
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app = QtWidgets.QApplication([])
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w = App(argv[1]) if len(argv) > 1 else App()
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exit(app.exec())
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if __name__ == '__main__':
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main()
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158
tiffexplore/tiffread.py
Normal file
158
tiffexplore/tiffread.py
Normal file
@@ -0,0 +1,158 @@
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import struct
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import tifffile
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import numpy as np
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class tiff():
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def __init__(self, file):
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self.file = file
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self.fh = open(file, 'rb')
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self.tiff = tifffile.TiffFile(self.file)
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self.tags = []
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self.get_file_len()
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self.addresses = assignments(len(self))
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nifd = self.read_header()
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i = 0
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while nifd:
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nifd = self.read_ifd(nifd, i)
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i += 1
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self.nifds = i
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for i, tags in enumerate(self.tags):
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if 273 in tags and 279 in tags:
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for j, a in enumerate(zip(tags[273][-1], tags[279][-1])):
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self.addresses[('image', i, j)] = a
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def get_file_len(self):
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self.fh.seek(0, 2)
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self.len = self.fh.tell()
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def __len__(self):
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return self.len
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def asarray(self, page, segment):
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return [d for d in zip(self.tiff.pages[page].segments(), range(segment + 1))][-1][0][0].squeeze()
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def read_header(self):
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self.fh.seek(0)
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self.byteorder = {b'II': '<', b'MM': '>'}[self.fh.read(2)]
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self.bigtiff = {42: False, 43: True}[struct.unpack(self.byteorder + 'H', self.fh.read(2))[0]]
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if self.bigtiff:
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self.tagsize = 20
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self.tagnoformat = 'Q'
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self.offsetsize = struct.unpack(self.byteorder + 'H', self.fh.read(2))[0]
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self.offsetformat = {8: 'Q', 16: '2Q'}[self.offsetsize]
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assert struct.unpack(self.byteorder + 'H', self.fh.read(2))[0] == 0, 'Not a TIFF-file'
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self.offset = struct.unpack(self.byteorder + self.offsetformat, self.fh.read(self.offsetsize))[0]
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else:
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self.tagsize = 12
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self.tagnoformat = 'H'
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self.offsetformat = 'I'
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self.offsetsize = 4
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self.offset = struct.unpack(self.byteorder + self.offsetformat, self.fh.read(self.offsetsize))[0]
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self.addresses[('header',)] = (0, 4 + self.bigtiff * 4 + self.offsetsize)
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return self.offset
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def read_ifd(self, offset, idx):
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""" Reads an IFD of the tiff file
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wp@tl20200214
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"""
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self.fh.seek(offset)
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nTags = struct.unpack(self.byteorder + self.tagnoformat, self.fh.read(struct.calcsize(self.tagnoformat)))[0]
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# print('Found {} tags'.format(nTags))
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assert nTags < 4096, 'Too many tags'
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length = 8 if self.bigtiff else 2
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length += nTags * self.tagsize + self.offsetsize
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||||
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||||
tags = {}
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for i in range(nTags):
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pos = offset + struct.calcsize(self.tagnoformat) + self.tagsize * i
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self.fh.seek(pos)
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||||
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||||
code, ttype = struct.unpack(self.byteorder + 'HH', self.fh.read(4))
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||||
count = struct.unpack(self.byteorder + self.offsetformat, self.fh.read(self.offsetsize))[0]
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||||
dtype = tifffile.TIFF.DATA_FORMATS[ttype]
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||||
dtypelen = struct.calcsize(dtype)
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||||
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toolong = struct.calcsize(dtype) * count > self.offsetsize
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if toolong:
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||||
caddr = struct.unpack(self.byteorder + self.offsetformat, self.fh.read(self.offsetsize))[0]
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||||
self.addresses[('tagdata', idx, code)] = (caddr, dtypelen * count)
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||||
cp = self.fh.tell()
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||||
self.fh.seek(caddr)
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||||
else:
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caddr = self.fh.tell()
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||||
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||||
if ttype == 1:
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||||
value = self.fh.read(count)
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||||
elif ttype == 2:
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||||
value = self.fh.read(count).decode('ascii').rstrip('\x00')
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||||
elif ttype == 5:
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||||
value = [struct.unpack(self.byteorder + dtype, self.fh.read(dtypelen)) for _ in range(count)]
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||||
else:
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||||
value = [struct.unpack(self.byteorder + dtype, self.fh.read(dtypelen))[0] for _ in range(count)]
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||||
|
||||
if toolong:
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||||
self.fh.seek(cp)
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||||
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||||
tags[code] = (ttype, caddr, dtypelen*count, value)
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||||
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||||
nifd = struct.unpack(self.byteorder + self.tagnoformat, self.fh.read(struct.calcsize(self.tagnoformat)))[0]
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||||
self.fh.seek(offset)
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||||
self.addresses[('ifd', idx)] = (offset, 2 * struct.calcsize(self.tagnoformat) + nTags * self.tagsize)
|
||||
self.tags.append(tags)
|
||||
return nifd
|
||||
|
||||
def __getitem__(self, item):
|
||||
if not isinstance(item, slice):
|
||||
item = slice(item, item+1)
|
||||
start = 0 if item.start is None or item.start < 0 else item.start
|
||||
step = item.step or 1
|
||||
stop = len(self) if item.stop is None or item.stop > len(self) else item.stop
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||||
self.fh.seek(start)
|
||||
return self.fh.read(stop - start)[::step]
|
||||
|
||||
def __enter__(self):
|
||||
return self
|
||||
|
||||
def __exit__(self, *args, **kwargs):
|
||||
self.tiff.close()
|
||||
self.close()
|
||||
|
||||
def close(self, *args, **kwargs):
|
||||
self.fh.close()
|
||||
|
||||
def get_bytes(self, part):
|
||||
offset, length = self.addresses[part]
|
||||
self.fh.seek(offset)
|
||||
return self.fh.read(length)
|
||||
|
||||
|
||||
class assignments(dict):
|
||||
def __init__(self, max_addr=0, *args, **kwargs):
|
||||
self.max_addr = max_addr
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
def get_assignment(self, addr):
|
||||
keys, values = zip(*self.items())
|
||||
offsets, lengths = zip(*values)
|
||||
offset_arr = np.array(offsets)
|
||||
offset_len = offset_arr + lengths
|
||||
nearest_addr = np.max(offset_arr[offset_arr <= addr])
|
||||
idxs = np.where(offset_arr == nearest_addr)[0]
|
||||
if addr < nearest_addr + lengths[idxs[0]]:
|
||||
return [(keys[idx], self[keys[idx]]) for idx in idxs]
|
||||
else:
|
||||
previous_addr = np.max(offset_len[offset_len <= addr])
|
||||
next_addr = offset_arr[offset_arr > addr]
|
||||
length = np.min(next_addr) - previous_addr if len(next_addr) else self.max_addr - previous_addr
|
||||
return [(('empty',), (previous_addr, length))]
|
||||
|
||||
def get_assignments(self, start=0, end=-1):
|
||||
addr = start
|
||||
if end == -1:
|
||||
end = self.max_addr
|
||||
while addr < end:
|
||||
item = self.get_assignment(addr)
|
||||
addr = sum(item[0][1])
|
||||
yield item
|
||||
Reference in New Issue
Block a user