pyqt5 code with astroalign not working after pyinstaller
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skyjudith JAI
Mar 16, 2025, 10:02:43 AMMar 16
to PyInstaller
I have tried to fix this problem for days with help from chatgpt, but without success. I wonder if anyone has ideas?
I'm on ubuntu working from a virtual environment. The code, Astro-FLEX.py, works fine when I just type python Astro-FLEX.py. The code opens a window, displays FITS files using astropy, and then runs astroalign to align the images. So all is well.
Now, when I run pyinstaller to create an executable, I cannot do the astroalign part. The code runs through the steps and creates a median at the end, but the actual shifting is not done. In the logger I get a message
I'm on ubuntu working from a virtual environment. The code, Astro-FLEX.py, works fine when I just type python Astro-FLEX.py. The code opens a window, displays FITS files using astropy, and then runs astroalign to align the images. So all is well.
Now, when I run pyinstaller to create an executable, I cannot do the astroalign part. The code runs through the steps and creates a median at the end, but the actual shifting is not done. In the logger I get a message
Error registering image filename.fit Input type for source not supported.
I am using
pyinstaller --onedir --add-data "/home/irwin/.local/lib/python3.10/site-packages/PyQt5/Qt5/plugins:PyQt5/Qt5/plugins" Astro-FLEX.py
but whether or not I include plugins, it still doesn't work.
I then booted on windows and get the same behaviour but no error message. Works fine from python but not after pyinstaller.
pyinstaller --onedir --add-data "/home/irwin/.local/lib/python3.10/site-packages/PyQt5/Qt5/plugins:PyQt5/Qt5/plugins" Astro-FLEX.py
but whether or not I include plugins, it still doesn't work.
I then booted on windows and get the same behaviour but no error message. Works fine from python but not after pyinstaller.
anyone have insight? thanks!
Judith
bwoodsend
Mar 16, 2025, 2:52:33 PMMar 16
to PyInstaller
Presumably whatever submodule/package/data file is responsible for supporting these FITS files is not being collected. I can't help beyond that without either a minimal example + FITS file to play with or a some clue as to what package/file is issuing that error message which will tell us where to look for what exactly is missing.
skyjudith JAI
Mar 16, 2025, 6:55:57 PMMar 16
to PyInstaller
My complete code is very long but I've made a 'minimumtest.py' which shows the same behaviour, i.e. works in python but fails after pyinstaller. The minimum code is below (sorry I don't see where I can include it as an attachment). I was aligning 9 fits images but each is 7.4 Mb. Is there somewhere I can put the fits files?
Judith
import sys
import os
import numpy as np
from astropy.io import fits
import astroalign as aa
from PyQt5.QtWidgets import (
QApplication, QMainWindow, QWidget, QVBoxLayout, QPushButton, QFileDialog, QLabel
)
from PyQt5.QtCore import QTimer
import pyqtgraph as pg
import warnings
warnings.simplefilter("ignore", DeprecationWarning)
class FITSAlignmentApp(QMainWindow):
def __init__(self):
super().__init__()
self.setWindowTitle("FITS Alignment Test")
self.setGeometry(100, 100, 800, 600)
# Main widget
central_widget = QWidget(self)
self.setCentralWidget(central_widget)
# Layout
layout = QVBoxLayout(central_widget)
# Load button
self.load_button = QPushButton("Load FITS Files", self)
self.load_button.clicked.connect(self.load_fits_files)
layout.addWidget(self.load_button)
# Status label
self.status_label = QLabel("Select FITS files to align", self)
layout.addWidget(self.status_label)
# PyQtGraph ImageView
self.image_view = pg.ImageView()
layout.addWidget(self.image_view)
# Timer for sequential loading
self.timer = QTimer()
self.timer.timeout.connect(self.show_next_image)
self.image_index = 0
self.images = []
self.aligned_images = []
self.transforms = []
def load_fits_files(self):
""" Open file dialog and load multiple FITS files with delay """
files, _ = QFileDialog.getOpenFileNames(
self, "Select FITS Files", os.getcwd(), # Start in the current working directory
"FITS Files (*.fits *.fit *.fts *.FITS *.FIT *.FTS);;All Files (*)"
)
if not files:
self.status_label.setText("No files selected.")
return
# Load images
self.images = []
for file in files:
try:
with fits.open(file) as hdul:
data = hdul[0].data
if data is not None:
self.images.append(data.astype(np.float64))
except Exception as e:
self.status_label.setText(f"Error loading {file}: {e}")
return
if len(self.images) < 2:
self.status_label.setText("Need at least 2 images to align.")
return
self.status_label.setText(f"Loaded {len(self.images)} images. Aligning...")
# Use the first image as the reference
self.reference_image = self.images[0]
self.aligned_images = [self.reference_image] # First image is already "aligned"
# Align each image to the reference
self.transforms = []
for i, img in enumerate(self.images[1:], start=1):
try:
# Compute the transformation parameters
transform, footprint = aa.find_transform(img, self.reference_image)
dx, dy = transform.translation # Extract x, y shifts
rotation_rad = transform.rotation # Extract rotation in radians
rotation_deg = np.degrees(rotation_rad) # Convert to degrees
# Apply the transformation to align the image
print(f"Original Image {i} Shape: {img.shape}")
aligned_img, footprint = aa.apply_transform(transform, img, self.reference_image)
# Ensure aligned_img is a NumPy array
aligned_img = np.array(aligned_img, dtype=np.float64)
print(f"Transformed Image {i} Shape: {aligned_img.shape}")
aligned_img = np.array(aligned_img, dtype=np.float64)
print(f"Image {i}: Δx = {dx:.2f}, Δy = {dy:.2f}, Δrot = {rotation_deg:.2f}°")
# Ensure aligned image has the same shape as the reference image
aligned_img = np.array(aligned_img, dtype=np.float64)
if aligned_img.shape != self.reference_image.shape:
print(f"Warning: Shape mismatch in Image {i}. Resizing...")
min_shape = (
min(aligned_img.shape[0], self.reference_image.shape[0]),
min(aligned_img.shape[1], self.reference_image.shape[1]),
)
aligned_img = aligned_img[:min_shape[0], :min_shape[1]]
self.reference_image = self.reference_image[:min_shape[0], :min_shape[1]]
self.aligned_images.append(aligned_img)
self.transforms.append(transform)
except Exception as e:
print(f"Error aligning image {i}: {e}")
self.aligned_images.append(img) # If alignment fails, keep original
self.status_label.setText("Alignment complete. Displaying images...")
self.image_index = 0
self.timer.start(1000) # 1-second delay between images
def extract_transform(self, transform):
""" Extract translation and rotation from transformation matrix. """
dx = transform[0, 2] # Translation in x
dy = transform[1, 2] # Translation in y
rotation_radians = np.arctan2(transform[1, 0], transform[0, 0])
rotation_degrees = np.degrees(rotation_radians) # Convert to degrees
return dx, dy, rotation_degrees
def show_next_image(self):
""" Show aligned images one by one before displaying the median """
if self.image_index < len(self.aligned_images):
current_image = self.aligned_images[self.image_index]
focus_min, focus_max = self.compute_focus_range(current_image)
self.image_view.setImage(current_image, levels=(focus_min, focus_max))
self.status_label.setText(f"Showing aligned image {self.image_index + 1}/{len(self.aligned_images)}")
self.image_index += 1
else:
# Stop the timer and compute the median
self.timer.stop()
self.display_median_image()
def display_median_image(self):
""" Compute and display the median-combined image """
self.status_label.setText("Computing median image...")
median_image = np.nanmedian(np.stack(self.aligned_images), axis=0)
focus_min, focus_max = self.compute_focus_range(median_image)
self.image_view.setImage(median_image, levels=(focus_min, focus_max))
self.status_label.setText("Showing median image.")
def compute_focus_range(self, data):
""" Compute focus_min and focus_max dynamically """
valid_data = data[data != 0] # Exclude exact zero values
if valid_data.size > 0:
median = np.nanmedian(valid_data)
std = np.nanstd(valid_data)
min_val = np.nanmin(valid_data)
max_val = np.nanmax(valid_data)
else:
# Fallback if all values are zero
median = np.nanmedian(data)
std = np.nanstd(data)
min_val = np.nanmin(data)
max_val = np.nanmax(data)
# Expand range slightly for better visualization
focus_min = max(median - std, min_val)
focus_max = min(median + std, max_val)
return focus_min, focus_max
if __name__ == "__main__":
app = QApplication(sys.argv)
window = FITSAlignmentApp()
window.show()
sys.exit(app.exec_())
import os
import numpy as np
from astropy.io import fits
import astroalign as aa
from PyQt5.QtWidgets import (
QApplication, QMainWindow, QWidget, QVBoxLayout, QPushButton, QFileDialog, QLabel
)
from PyQt5.QtCore import QTimer
import pyqtgraph as pg
import warnings
warnings.simplefilter("ignore", DeprecationWarning)
class FITSAlignmentApp(QMainWindow):
def __init__(self):
super().__init__()
self.setWindowTitle("FITS Alignment Test")
self.setGeometry(100, 100, 800, 600)
# Main widget
central_widget = QWidget(self)
self.setCentralWidget(central_widget)
# Layout
layout = QVBoxLayout(central_widget)
# Load button
self.load_button = QPushButton("Load FITS Files", self)
self.load_button.clicked.connect(self.load_fits_files)
layout.addWidget(self.load_button)
# Status label
self.status_label = QLabel("Select FITS files to align", self)
layout.addWidget(self.status_label)
# PyQtGraph ImageView
self.image_view = pg.ImageView()
layout.addWidget(self.image_view)
# Timer for sequential loading
self.timer = QTimer()
self.timer.timeout.connect(self.show_next_image)
self.image_index = 0
self.images = []
self.aligned_images = []
self.transforms = []
def load_fits_files(self):
""" Open file dialog and load multiple FITS files with delay """
files, _ = QFileDialog.getOpenFileNames(
self, "Select FITS Files", os.getcwd(), # Start in the current working directory
"FITS Files (*.fits *.fit *.fts *.FITS *.FIT *.FTS);;All Files (*)"
)
if not files:
self.status_label.setText("No files selected.")
return
# Load images
self.images = []
for file in files:
try:
with fits.open(file) as hdul:
data = hdul[0].data
if data is not None:
self.images.append(data.astype(np.float64))
except Exception as e:
self.status_label.setText(f"Error loading {file}: {e}")
return
if len(self.images) < 2:
self.status_label.setText("Need at least 2 images to align.")
return
self.status_label.setText(f"Loaded {len(self.images)} images. Aligning...")
# Use the first image as the reference
self.reference_image = self.images[0]
self.aligned_images = [self.reference_image] # First image is already "aligned"
# Align each image to the reference
self.transforms = []
for i, img in enumerate(self.images[1:], start=1):
try:
# Compute the transformation parameters
transform, footprint = aa.find_transform(img, self.reference_image)
dx, dy = transform.translation # Extract x, y shifts
rotation_rad = transform.rotation # Extract rotation in radians
rotation_deg = np.degrees(rotation_rad) # Convert to degrees
# Apply the transformation to align the image
print(f"Original Image {i} Shape: {img.shape}")
aligned_img, footprint = aa.apply_transform(transform, img, self.reference_image)
# Ensure aligned_img is a NumPy array
aligned_img = np.array(aligned_img, dtype=np.float64)
print(f"Transformed Image {i} Shape: {aligned_img.shape}")
aligned_img = np.array(aligned_img, dtype=np.float64)
print(f"Image {i}: Δx = {dx:.2f}, Δy = {dy:.2f}, Δrot = {rotation_deg:.2f}°")
# Ensure aligned image has the same shape as the reference image
aligned_img = np.array(aligned_img, dtype=np.float64)
if aligned_img.shape != self.reference_image.shape:
print(f"Warning: Shape mismatch in Image {i}. Resizing...")
min_shape = (
min(aligned_img.shape[0], self.reference_image.shape[0]),
min(aligned_img.shape[1], self.reference_image.shape[1]),
)
aligned_img = aligned_img[:min_shape[0], :min_shape[1]]
self.reference_image = self.reference_image[:min_shape[0], :min_shape[1]]
self.aligned_images.append(aligned_img)
self.transforms.append(transform)
except Exception as e:
print(f"Error aligning image {i}: {e}")
self.aligned_images.append(img) # If alignment fails, keep original
self.status_label.setText("Alignment complete. Displaying images...")
self.image_index = 0
self.timer.start(1000) # 1-second delay between images
def extract_transform(self, transform):
""" Extract translation and rotation from transformation matrix. """
dx = transform[0, 2] # Translation in x
dy = transform[1, 2] # Translation in y
rotation_radians = np.arctan2(transform[1, 0], transform[0, 0])
rotation_degrees = np.degrees(rotation_radians) # Convert to degrees
return dx, dy, rotation_degrees
def show_next_image(self):
""" Show aligned images one by one before displaying the median """
if self.image_index < len(self.aligned_images):
current_image = self.aligned_images[self.image_index]
focus_min, focus_max = self.compute_focus_range(current_image)
self.image_view.setImage(current_image, levels=(focus_min, focus_max))
self.status_label.setText(f"Showing aligned image {self.image_index + 1}/{len(self.aligned_images)}")
self.image_index += 1
else:
# Stop the timer and compute the median
self.timer.stop()
self.display_median_image()
def display_median_image(self):
""" Compute and display the median-combined image """
self.status_label.setText("Computing median image...")
median_image = np.nanmedian(np.stack(self.aligned_images), axis=0)
focus_min, focus_max = self.compute_focus_range(median_image)
self.image_view.setImage(median_image, levels=(focus_min, focus_max))
self.status_label.setText("Showing median image.")
def compute_focus_range(self, data):
""" Compute focus_min and focus_max dynamically """
valid_data = data[data != 0] # Exclude exact zero values
if valid_data.size > 0:
median = np.nanmedian(valid_data)
std = np.nanstd(valid_data)
min_val = np.nanmin(valid_data)
max_val = np.nanmax(valid_data)
else:
# Fallback if all values are zero
median = np.nanmedian(data)
std = np.nanstd(data)
min_val = np.nanmin(data)
max_val = np.nanmax(data)
# Expand range slightly for better visualization
focus_min = max(median - std, min_val)
focus_max = min(median + std, max_val)
return focus_min, focus_max
if __name__ == "__main__":
app = QApplication(sys.argv)
window = FITSAlignmentApp()
window.show()
sys.exit(app.exec_())
Chris Barker
Mar 17, 2025, 5:06:00 PMMar 17
to pyins...@googlegroups.com
Just a suggestion- to make it even easier to diagnose, try a simple script only processes a fits file, without QT.
That will be a far simpler build, and it may be more obvious what’s missing.
-CHB
Christopher Barker, Ph.D.
Oceanographer
Emergency Response Division
NOAA/NOS/OR&R (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chris....@noaa.gov
Christopher Barker, Ph.D.
Oceanographer
Emergency Response Division
NOAA/NOS/OR&R (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chris....@noaa.gov
--
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skyjudith JAI
Mar 18, 2025, 9:30:44 AMMar 18
to pyins...@googlegroups.com
so far no success. I've pared everything down to the simplest possible code. The code is attached.
typing
python simple_align.py BG1.FIT BG2.FIT
gives output indicating that the alignment works fine.
however, after
pyinstaller --onedir --clean \
--hidden-import=numpy \
--hidden-import=astropy \
--hidden-import=astroalign \
--hidden-import=skimage \
--collect-all sep \
--copy-metadata sep \
--exclude-module=cv2 \
simple_align.py
--hidden-import=numpy \
--hidden-import=astropy \
--hidden-import=astroalign \
--hidden-import=skimage \
--collect-all sep \
--copy-metadata sep \
--exclude-module=cv2 \
simple_align.py
then going to the dist directory
./simple_align BG1.FIT BG2.FIT
I get
Error during alignment: Input type for source not supported.
It looks like I need to send the 2 fits files in 2 more posts, since they are too large for one message.
Judith
To view this discussion visit https://groups.google.com/d/msgid/pyinstaller/CALGmxE%2Bs7_q-cwRTU7abB3HYR3V2YjArywUQj_NyK2yZztSSag%40mail.gmail.com.
skyjudith JAI
Mar 18, 2025, 9:31:53 AMMar 18
to pyins...@googlegroups.com
Here is the first fits file.
On Mon, Mar 17, 2025 at 5:05 PM 'Chris Barker' via PyInstaller <pyins...@googlegroups.com> wrote:
To view this discussion visit https://groups.google.com/d/msgid/pyinstaller/CALGmxE%2Bs7_q-cwRTU7abB3HYR3V2YjArywUQj_NyK2yZztSSag%40mail.gmail.com.
skyjudith JAI
Mar 18, 2025, 9:32:31 AMMar 18
to pyins...@googlegroups.com
Here is the second fits file.
On Mon, Mar 17, 2025 at 5:05 PM 'Chris Barker' via PyInstaller <pyins...@googlegroups.com> wrote:
To view this discussion visit https://groups.google.com/d/msgid/pyinstaller/CALGmxE%2Bs7_q-cwRTU7abB3HYR3V2YjArywUQj_NyK2yZztSSag%40mail.gmail.com.
Chris Barker
Mar 18, 2025, 11:03:44 AMMar 18
to pyins...@googlegroups.com
If seems the first decider us not being included by installer-. I would ask the astropy folks where/how the decoders are discovered.
In the meantime, maybe try setting astropy.io or even astropy.io.fits as a hidden import.
Though if you aren’t getting an import error, then the (python) module is there — but it seems to rely on a data file, or library or something that isn’t being included.
Though if you aren’t getting an import error, then the (python) module is there — but it seems to rely on a data file, or library or something that isn’t being included.
-CHB
Christopher Barker, Ph.D.
Oceanographer
Emergency Response Division
NOAA/NOS/OR&R (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chris....@noaa.gov
To view this discussion visit https://groups.google.com/d/msgid/pyinstaller/CABuiZshvX0h0O2M6yJBQx8o-Oh4fBVoiVWcvyY0M2iXaLHQDdg%40mail.gmail.com.
bwoodsend
Mar 18, 2025, 3:04:45 PMMar 18
to PyInstaller
If you remove the try/except, the cause is fairly standard.
Traceback (most recent call last): File "astroalign.py", line 537, in _find_sources File "sep_pjw.pyx", line 21, in init sep_pjw ModuleNotFoundError: No module named '_version' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "simple_align.py", line 25, in <module> transform, footprint = aa.find_transform(target_image, ref_image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "astroalign.py", line 314, in find_transform TypeError: Input type for source not supported. [PYI-1439842:ERROR] Failed to execute script 'simple_align' due to unhandled exception!The fix is just to add --hiddenimport=_version to the build command. (I’d call it a bug in sep_pjw that it’s keeping its version in a top level module rather than say sep_pjw._version but that’s another matter.)
Please never use blanket exception handling like that. We’d have fixed this in about 2 seconds if you hadn’t thrown away the stacktrace.
Chris Barker
Mar 18, 2025, 3:34:13 PMMar 18
to pyins...@googlegroups.com
he fix is just to add --hiddenimport=_version to the build command. (I’d call it a bug in sep_pjw that it’s keeping its version in a top level module rather than say sep_pjw._version but that’s another matter.)
good point -- I took a look at sep_pjw to see if I could report this, but:
The
So maybe give sep a try ... it may not have this issue.
sep-pjw package was deprecated on 03/02/2025, and is now published under the original sep name. Please install sep>=1.4.0 instead. Future development will take place at sep-developers/sep.So maybe give sep a try ... it may not have this issue.
-CHB
Please never use blanket exception handling like that. We’d have fixed this in about 2 seconds if you hadn’t thrown away the stacktrace.
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skyjudith JAI
Mar 19, 2025, 9:50:20 AMMar 19
to pyins...@googlegroups.com
Thank you! Brilliant. That worked. It's something that I (and my on-again off-again friend chatgpt) did not figure out. Could you explain what you mean by:
"Please never use blanket exception handling like that." I"m not sure what the alternative should be.
Judith
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Chris Barker
Mar 19, 2025, 12:09:20 PMMar 19
to pyins...@googlegroups.com
On Wed, Mar 19, 2025 at 6:50 AM skyjudith JAI <skyla...@gmail.com> wrote:
Thank you! Brilliant. That worked. It's something that I (and my on-again off-again friend chatgpt) did not figure out. Could you explain what you mean by:"Please never use blanket exception handling like that." I"m not sure what the alternative should be.
What he means is that:
except Exception as e:
print("Error during alignment:", e)Will catch ANY exception, and then swallow it up to make it go away, leaving you with no idea what went wrong.
So better to maybe catch, print a helpful message and then re-raise the exception so you'll get the full stack trace.
In practice, particularly behind a GUI, there may be a need for your program not to crash out. In that cse, you want to capture and log or print, or something, the full traceback. Google for how, but here's a hint:
https://docs.python.org/3/library/traceback.html#module-traceback
https://docs.python.org/3/library/traceback.html#module-traceback
Meanwhile, when debugging, you definitely simply want the Exception to bubble up :-)
-CHB
Judith--On Tue, Mar 18, 2025 at 3:04 PM bwoodsend <bwoo...@gmail.com> wrote:--If you remove the try/except, the cause is fairly standard.
Traceback (most recent call last): File "astroalign.py", line 537, in _find_sources File "sep_pjw.pyx", line 21, in init sep_pjw ModuleNotFoundError: No module named '_version' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "simple_align.py", line 25, in <module> transform, footprint = aa.find_transform(target_image, ref_image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "astroalign.py", line 314, in find_transform TypeError: Input type for source not supported. [PYI-1439842:ERROR] Failed to execute script 'simple_align' due to unhandled exception!The fix is just to add --hiddenimport=_version to the build command. (I’d call it a bug in sep_pjw that it’s keeping its version in a top level module rather than say sep_pjw._version but that’s another matter.)
Please never use blanket exception handling like that. We’d have fixed this in about 2 seconds if you hadn’t thrown away the stacktrace.
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