Changwanseo
commented
1 year ago That happens because qt dependency works different from when ete3 has built The standard tactic is to revert pyqt5 version to previous, but I had hard time solving multiple it.
The heuristic, is to add underlying code in front of your code. It will change how ete3 render works.
# ete3 patch
from __future__ import absolute_import
from __future__ import print_function
import ete3
# Patch for ete3 3.1.2 colliding with higher version PyQt5
def save(scene, imgName, w=None, h=None, dpi=90, take_region=False, units="px"):
import colorsys
import random
import re
import types
from sys import stderr
from PyQt5 import QtGui, QtCore
from PyQt5.QtCore import (
Qt,
QPointF,
QRect,
QRectF,
QBuffer,
QByteArray,
QThread,
QIODevice,
QMetaObject,
QModelIndex,
QObject,
QRegExp,
QSize,
QSizeF,
QVariant,
) # QString
from PyQt5.QtSvg import QGraphicsSvgItem, QSvgGenerator
from PyQt5.QtOpenGL import QGLFormat, QGLWidget
from PyQt5.QtPrintSupport import QPrinter
from PyQt5.QtWidgets import (
QAction,
QApplication,
QCheckBox,
QWidget,
QColorDialog,
QComboBox,
QDialog,
QDialogButtonBox,
QFileDialog,
QGraphicsEllipseItem,
QGraphicsItem,
QGraphicsItemGroup,
QGraphicsLineItem,
QGraphicsPathItem,
QGraphicsPixmapItem,
QGraphicsPolygonItem,
QGraphicsRectItem,
QGraphicsScene,
QGraphicsSimpleTextItem,
QGraphicsTextItem,
QGraphicsView,
QInputDialog,
QItemDelegate,
QLabel,
QLineEdit,
QListWidget,
QMainWindow,
QMenu,
QMenuBar,
QMessageBox,
QPushButton,
QSplitter,
QStatusBar,
QTableView,
QTextEdit,
QToolBar,
QVBoxLayout,
QWidget,
)
from PyQt5.QtGui import (
QBrush,
QColor,
QCursor,
QFont,
QFontMetrics,
QIcon,
QImage,
QPainter,
QPainterPath,
QPen,
QPixmap,
QPolygonF,
QRadialGradient,
QRegExpValidator,
QStandardItemModel,
QTransform,
)
QtCore.pyqtSignature = QtCore.pyqtSlot
from ete3.treeview.svg_colors import SVG_COLORS, COLOR_SCHEMES
import time
ipython_inline = False
if imgName == "%%inline":
ipython_inline = True
ext = "PNG"
elif imgName == "%%inlineSVG":
ipython_inline = True
ext = "SVG"
elif imgName.startswith("%%return"):
try:
ext = imgName.split(".")[1].upper()
except IndexError:
ext = "SVG"
imgName = "%%return"
else:
ext = imgName.split(".")[-1].upper()
main_rect = scene.sceneRect()
aspect_ratio = main_rect.height() / main_rect.width()
# auto adjust size
if not w and not h:
units = "px"
w = main_rect.width()
h = main_rect.height()
ratio_mode = Qt.KeepAspectRatio
elif w and h:
ratio_mode = Qt.IgnoreAspectRatio
elif h is None:
h = w * aspect_ratio
ratio_mode = Qt.KeepAspectRatio
elif w is None:
w = h / aspect_ratio
ratio_mode = Qt.KeepAspectRatio
# Adjust to resolution
if units == "mm":
if w:
w = w * 0.0393700787 * dpi
if h:
h = h * 0.0393700787 * dpi
elif units == "in":
if w:
w = w * dpi
if h:
h = h * dpi
elif units == "px":
pass
else:
raise Exception("wrong unit format")
x_scale, y_scale = w / main_rect.width(), h / main_rect.height()
if ext == "SVG":
svg = QSvgGenerator()
targetRect = QRectF(0, 0, w, h)
svg.setSize(QSize(int(w), int(h)))
svg.setViewBox(targetRect)
svg.setTitle("Generated with ETE http://etetoolkit.org")
svg.setDescription("Generated with ETE http://etetoolkit.org")
if imgName == "%%return":
ba = QByteArray()
buf = QBuffer(ba)
buf.open(QIODevice.WriteOnly)
svg.setOutputDevice(buf)
else:
svg.setFileName(imgName)
pp = QPainter()
pp.begin(svg)
scene.render(pp, targetRect, scene.sceneRect(), ratio_mode)
pp.end()
if imgName == "%%return":
compatible_code = str(ba)
print("from memory")
else:
compatible_code = open(imgName).read()
# Fix a very annoying problem with Radial gradients in
# inkscape and browsers...
compatible_code = compatible_code.replace("xml:id=", "id=")
compatible_code = re.sub(
'font-size="(\d+)"', 'font-size="\\1pt"', compatible_code
)
compatible_code = compatible_code.replace("\n", " ")
compatible_code = re.sub("<g [^>]+>\s*</g>", "", compatible_code)
# End of fix
if ipython_inline:
from IPython.core.display import SVG
return SVG(compatible_code)
elif imgName == "%%return":
return x_scale, y_scale, compatible_code
else:
open(imgName, "w").write(compatible_code)
elif ext == "PDF" or ext == "PS":
if ext == "PS":
format = QPrinter.PostScriptFormat
else:
format = QPrinter.PdfFormat
printer = QPrinter(QPrinter.HighResolution)
printer.setResolution(dpi)
printer.setOutputFormat(format)
printer.setPageSize(QPrinter.A4)
printer.setPaperSize(QSizeF(w, h), QPrinter.DevicePixel)
printer.setPageMargins(0, 0, 0, 0, QPrinter.DevicePixel)
# pageTopLeft = printer.pageRect().topLeft()
# paperTopLeft = printer.paperRect().topLeft()
# For PS -> problems with margins
# print paperTopLeft.x(), paperTopLeft.y()
# print pageTopLeft.x(), pageTopLeft.y()
# print printer.paperRect().height(), printer.pageRect().height()
# topleft = pageTopLeft - paperTopLeft
printer.setFullPage(True)
printer.setOutputFileName(imgName)
pp = QPainter(printer)
targetRect = QRectF(0, 0, w, h)
scene.render(pp, targetRect, scene.sceneRect(), ratio_mode)
else:
targetRect = QRectF(0, 0, w, h)
ii = QImage(w, h, QImage.Format_ARGB32)
ii.fill(QColor(Qt.white).rgb())
ii.setDotsPerMeterX(dpi / 0.0254) # Convert inches to meters
ii.setDotsPerMeterY(dpi / 0.0254)
pp = QPainter(ii)
pp.setRenderHint(QPainter.Antialiasing)
pp.setRenderHint(QPainter.TextAntialiasing)
pp.setRenderHint(QPainter.SmoothPixmapTransform)
scene.render(pp, targetRect, scene.sceneRect(), ratio_mode)
pp.end()
if ipython_inline:
ba = QByteArray()
buf = QBuffer(ba)
buf.open(QIODevice.WriteOnly)
ii.save(buf, "PNG")
from IPython.core.display import Image
return Image(ba.data())
elif imgName == "%%return":
ba = QByteArray()
buf = QBuffer(ba)
buf.open(QIODevice.WriteOnly)
ii.save(buf, "PNG")
return x_scale, y_scale, ba.toBase64()
else:
ii.save(imgName)
return w / main_rect.width(), h / main_rect.height()
def patch():
ete3.treeview.main.save = save
patch()
mlarjim
Hi, I am getting the following error when using treeview:
Could you please fix this? Thank you!!