When I run my code from Pyinstaller the tiff reader works fine. After freezing using Pyinstaller I get the following warning:
UserWarning: ImportError: No module named '_tifffile'. Loading of some compressed images will be very slow. Tifffile.c can be obtained at http://www.lfd.uci.edu/~gohlke
And sure enough, a tiff file that used to take seconds to load into a numpy array may now take minutes.
Here is a simplified form of my code to focus on the problem. If you load an example tiff like this one it should load fast without problems.
If you use C:\Python35\python.exe C:\Python35\Scripts\pyinstaller.exe --additional-hooks-dir=. --clean --win-private-assemblies tiffile_problems.py you should get a functional .exe with the above error message when you run it. When you try to load the same tiff it now takes much longer.
tiffile_problems.py
#!/usr/bin/env python3
import os
import sys
import traceback
import numpy as np
import matplotlib.pyplot as plt
from PyQt4.QtGui import *
from PyQt4.QtCore import *
sys.path.append('..')
from MBE_for_SO.util import fileloader, fileconverter
class NotConvertedError(Exception):
pass
class FileAlreadyInProjectError(Exception):
def __init__(self, filename):
self.filename = filename
class Widget(QWidget):
def __init__(self, project, parent=None):
super(Widget, self).__init__(parent)
if not project:
self.setup_ui()
return
def setup_ui(self):
vbox = QVBoxLayout()
## Related to importing Raws
self.setWindowTitle('Import Raw File')
#vbox.addWidget(QLabel('Set the size all data are to be rescaled to'))
grid = QGridLayout()
vbox.addLayout(grid)
vbox.addStretch()
self.setLayout(vbox)
self.resize(400, 220)
self.listview = QListView()
self.listview.setStyleSheet('QListView::item { height: 26px; }')
self.listview.setSelectionMode(QAbstractItemView.NoSelection)
vbox.addWidget(self.listview)
hbox = QVBoxLayout()
pb = QPushButton('New Video')
pb.clicked.connect(self.new_video)
hbox.addWidget(pb)
vbox.addLayout(hbox)
vbox.addStretch()
self.setLayout(vbox)
def convert_tif(self, filename):
path = os.path.splitext(os.path.basename(filename))[0] + '.npy'
#path = os.path.join(self.project.path, path)
progress = QProgressDialog('Converting tif to npy...', 'Abort', 0, 100, self)
progress.setAutoClose(True)
progress.setMinimumDuration(0)
progress.setValue(0)
def callback(value):
progress.setValue(int(value * 100))
QApplication.processEvents()
try:
fileconverter.tif2npy(filename, path, callback)
print('Tifffile saved to wherever this script is')
except:
# qtutil.critical('Converting tiff to npy failed.')
progress.close()
return path
def to_npy(self, filename):
if filename.endswith('.raw'):
print('No raws allowed')
#filename = self.convert_raw(filename)
elif filename.endswith('.tif'):
filename = self.convert_tif(filename)
else:
raise fileloader.UnknownFileFormatError()
return filename
def import_file(self, filename):
if not filename.endswith('.npy'):
new_filename = self.to_npy(filename)
if not new_filename:
raise NotConvertedError()
else:
filename = new_filename
return filename
def import_files(self, filenames):
for filename in filenames:
try:
filename = self.import_file(filename)
except NotConvertedError:
# qtutil.warning('Skipping file \'{}\' since not converted.'.format(filename))
print('Skipping file \'{}\' since not converted.'.format(filename))
except FileAlreadyInProjectError as e:
# qtutil.warning('Skipping file \'{}\' since already in project.'.format(e.filename))
print('Skipping file \'{}\' since already in project.'.format(e.filename))
except:
# qtutil.critical('Import of \'{}\' failed:\n'.format(filename) +\
# traceback.format_exc())
print('Import of \'{}\' failed:\n'.format(filename) + traceback.format_exc())
# else:
# self.listview.model().appendRow(QStandardItem(filename))
def new_video(self):
filenames = QFileDialog.getOpenFileNames(
self, 'Load images', QSettings().value('last_load_data_path'),
'Video files (*.npy *.tif *.raw)')
if not filenames:
return
QSettings().setValue('last_load_data_path', os.path.dirname(filenames[0]))
self.import_files(filenames)
class MyPlugin:
def __init__(self, project):
self.name = 'Import video files'
self.widget = Widget(project)
def run(self):
pass
if __name__ == '__main__':
app = QApplication(sys.argv)
app.aboutToQuit.connect(app.deleteLater)
w = QMainWindow()
w.setCentralWidget(Widget(None))
w.show()
app.exec_()
sys.exit()
fileconverter.py
#!/usr/bin/env python3
import os
import numpy as np
import tifffile as tiff
class ConvertError(Exception):
pass
def tif2npy(filename_from, filename_to, progress_callback):
with tiff.TiffFile(filename_from) as tif:
w, h = tif[0].shape
shape = len(tif), w, h
np.save(filename_to, np.empty(shape, tif[0].dtype))
fp = np.load(filename_to, mmap_mode='r+')
for i, page in enumerate(tif):
progress_callback(i / float(shape[0]-1))
fp[i] = page.asarray()
def raw2npy(filename_from, filename_to, dtype, width, height,
num_channels, channel, progress_callback):
fp = np.memmap(filename_from, dtype, 'r')
frame_size = width * height * num_channels
if len(fp) % frame_size:
raise ConvertError()
num_frames = len(fp) / frame_size
fp = np.memmap(filename_from, dtype, 'r',
shape=(num_frames, width, height, num_channels))
np.save(filename_to, np.empty((num_frames, width, height), dtype))
fp_to = np.load(filename_to, mmap_mode='r+')
for i, frame in enumerate(fp):
progress_callback(i / float(len(fp)-1))
fp_to[i] = frame[:,:,channel-1]
fileloader.py
#!/usr/bin/env python3
import numpy as np
class UnknownFileFormatError(Exception):
pass
def load_npy(filename):
frames = np.load(filename)
# frames[np.isnan(frames)] = 0
return frames
def load_file(filename):
if filename.endswith('.npy'):
frames = load_npy(filename)
else:
raise UnknownFileFormatError()
return frames
def load_reference_frame_npy(filename, offset):
frames_mmap = np.load(filename, mmap_mode='c')
if frames_mmap is None:
return None
frame = np.array(frames_mmap[offset])
frame[np.isnan(frame)] = 0
frame = frame.swapaxes(0, 1)
if frame.ndim == 2:
frame = frame[:, ::-1]
elif frame.ndim == 3:
frame = frame[:, ::-1, :]
return frame
def load_reference_frame(filename, offset=0):
if filename.endswith('.npy'):
frame = load_reference_frame_npy(filename, offset)
else:
raise UnknownFileFormatError()
return frame
Why? And how do I fix this? I've located tifffile.py, tifffile.cpython-35.pyc, tifffile.c and placed them all in the same directory as the .exe. No effect. _tifffile.cp35-win_amd64.pyd is created by pyinstaller and placed in the same dir as the .exe. I don't know what other options are available to me.
tifffile_problems.spec
# -*- mode: python -*-
block_cipher = None
a = Analysis(['tiffile_problems.py'],
pathex=['C:\\Users\\Cornelis\\PycharmProjects\\tester\\MBE_for_SO'],
binaries=None,
datas=None,
hiddenimports=[],
hookspath=[],
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=True,
cipher=block_cipher)
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz,
a.scripts,
exclude_binaries=True,
name='tiffile_problems',
debug=False,
strip=False,
upx=True,
console=True )
coll = COLLECT(exe,
a.binaries,
a.zipfiles,
a.datas,
strip=False,
upx=True,
name='tiffile_problems')
tiffile.spec when using C:\Python35\python.exe C:\Python35\Scripts\pyinstaller.exe --additional-hooks-dir=. --clean --win-private-assemblies --onefile tiffile_problems.py
# -*- mode: python -*-
block_cipher = None
a = Analysis(['tiffile_problems.py'],
pathex=['C:\\Users\\Cornelis\\PycharmProjects\\tester\\MBE_for_SO'],
binaries=None,
datas=None,
hiddenimports=[],
hookspath=['.'],
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=True,
cipher=block_cipher)
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz,
a.scripts,
a.binaries,
a.zipfiles,
a.datas,
name='tiffile_problems',
debug=False,
strip=False,
upx=True,
console=True )
