shinestacker 1.8.0__py3-none-any.whl → 1.9.0__py3-none-any.whl

shinestacker/algorithms/exif.py

@@ -1,12 +1,14 @@
-# pylint: disable=C0114, C0116, W0718, R0911, R0912, E1101
+# pylint: disable=C0114, C0116, W0718, R0911, R0912, E1101, R0915, R1702, R0914, R0917, R0913
 import os
 import re
 import io
 import logging
+import traceback
 import cv2
 import numpy as np
 from PIL import Image
 from PIL.TiffImagePlugin import IFDRational
+from PIL.PngImagePlugin import PngInfo
 from PIL.ExifTags import TAGS
 import tifffile
 from .. config.constants import constants
@@ -58,9 +60,33 @@ def get_exif(exif_filename):
             if data is not None:
                 exif_data[XMLPACKET] = data
         return exif_data
+    if extension_png(exif_filename):
+        exif_data = get_exif_from_png(image)
+        return exif_data if exif_data else image.getexif()
     return image.getexif()
 
 
+def get_exif_from_png(image):
+    exif_data = {}
+    try:
+        exif_from_image = image.getexif()
+        if exif_from_image:
+            exif_data.update(dict(exif_from_image))
+    except Exception:
+        pass
+    try:
+        if hasattr(image, 'text') and image.text:
+            for key, value in image.text.items():
+                exif_data[f"PNG_{key}"] = value
+        if hasattr(image, 'info') and image.info:
+            for key, value in image.info.items():
+                if key not in ['dpi', 'gamma']:
+                    exif_data[f"PNG_{key}"] = value
+    except Exception:
+        pass
+    return exif_data
+
+
 def exif_extra_tags_for_tif(exif):
     logger = logging.getLogger(__name__)
     res_x, res_y = exif.get(RESOLUTIONX), exif.get(RESOLUTIONY)
@@ -153,7 +179,222 @@ def add_exif_data_to_jpg_file(exif, in_filenama, out_filename, verbose=False):
     return exif
 
 
-def write_image_with_exif_data(exif, image, out_filename, verbose=False):
+def create_xmp_from_exif(exif_data):
+    xmp_elements = []
+    if exif_data:
+        for tag_id, value in exif_data.items():
+            if isinstance(tag_id, int):
+                if tag_id == 270 and value:  # ImageDescription
+                    desc = value
+                    if isinstance(desc, bytes):
+                        desc = desc.decode('utf-8', errors='ignore')
+                    xmp_elements.append(
+                        f'<dc:description><rdf:Alt><rdf:li xml:lang="x-default">{desc}</rdf:li>'
+                        '</rdf:Alt></dc:description>')
+                elif tag_id == 315 and value:  # Artist
+                    artist = value
+                    if isinstance(artist, bytes):
+                        artist = artist.decode('utf-8', errors='ignore')
+                    xmp_elements.append(
+                        f'<dc:creator><rdf:Seq><rdf:li>{artist}</rdf:li>'
+                        '</rdf:Seq></dc:creator>')
+                elif tag_id == 33432 and value:  # Copyright
+                    copyright_tag = value
+                    if isinstance(copyright_tag, bytes):
+                        copyright_tag = copyright_tag.decode('utf-8', errors='ignore')
+                    xmp_elements.append(
+                        f'<dc:rights><rdf:Alt><rdf:li xml:lang="x-default">{copyright_tag}</rdf:li>'
+                        '</rdf:Alt></dc:rights>')
+                elif tag_id == 271 and value:  # Make
+                    make = value
+                    if isinstance(make, bytes):
+                        make = make.decode('utf-8', errors='ignore')
+                    xmp_elements.append(f'<tiff:Make>{make}</tiff:Make>')
+                elif tag_id == 272 and value:  # Model
+                    model = value
+                    if isinstance(model, bytes):
+                        model = model.decode('utf-8', errors='ignore')
+                    xmp_elements.append(f'<tiff:Model>{model}</tiff:Model>')
+                elif tag_id == 306 and value:  # DateTime
+                    datetime_val = value
+                    if isinstance(datetime_val, bytes):
+                        datetime_val = datetime_val.decode('utf-8', errors='ignore')
+                    if ':' in datetime_val:
+                        datetime_val = datetime_val.replace(':', '-', 2).replace(' ', 'T')
+                    xmp_elements.append(f'<xmp:CreateDate>{datetime_val}</xmp:CreateDate>')
+                elif tag_id == 305 and value:  # Software
+                    software = value
+                    if isinstance(software, bytes):
+                        software = software.decode('utf-8', errors='ignore')
+                    xmp_elements.append(f'<xmp:CreatorTool>{software}</xmp:CreatorTool>')
+    if xmp_elements:
+        xmp_content = '\n    '.join(xmp_elements)
+        xmp_template = f"""<?xpacket begin='' id='W5M0MpCehiHzreSzNTczkc9d'?>
+<x:xmpmeta xmlns:x='adobe:ns:meta/'
+ x:xmptk='Adobe XMP Core 5.6-c140 79.160451, 2017/05/06-01:08:21'>
+ <rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
+  <rdf:Description rdf:about=''
+    xmlns:dc='http://purl.org/dc/elements/1.1/'
+    xmlns:xmp='http://ns.adobe.com/xap/1.0/'
+    xmlns:tiff='http://ns.adobe.com/tiff/1.0/'
+    xmlns:exif='http://ns.adobe.com/exif/1.0/'>
+    {xmp_content}
+  </rdf:Description>
+ </rdf:RDF>
+</x:xmpmeta>
+<?xpacket end='w'?>"""
+        return xmp_template
+    return """<?xpacket begin='' id='W5M0MpCehiHzreSzNTczkc9d'?>
+<x:xmpmeta xmlns:x='adobe:ns:meta/'
+ x:xmptk='Adobe XMP Core 5.6-c140 79.160451, 2017/05/06-01:08:21'>
+ <rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
+  <rdf:Description rdf:about=''/>
+ </rdf:RDF>
+</x:xmpmeta>
+<?xpacket end='w'?>"""
+
+
+def write_image_with_exif_data_png(exif, image, out_filename, verbose=False, color_order='auto'):
+    logger = logging.getLogger(__name__)
+    if isinstance(image, np.ndarray) and image.dtype == np.uint16:
+        if verbose:
+            logger.warning(msg="EXIF data not supported for 16-bit PNG format")
+        write_img(out_filename, image)
+        return
+    pil_image = _convert_to_pil_image(image, color_order, verbose, logger)
+    pnginfo, icc_profile = _prepare_png_metadata(exif, verbose, logger)
+    _save_png_with_metadata(pil_image, out_filename, pnginfo, icc_profile, verbose, logger)
+
+
+def _convert_to_pil_image(image, color_order, verbose, logger):
+    if isinstance(image, np.ndarray):
+        if len(image.shape) == 3 and image.shape[2] == 3:
+            if color_order in ['auto', 'bgr']:
+                image_rgb = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)
+                if verbose:
+                    logger.info(msg="Converted BGR to RGB for PIL")
+                return Image.fromarray(image_rgb)
+        return Image.fromarray(image)
+    return image
+
+
+def _prepare_png_metadata(exif, verbose, logger):
+    pnginfo = PngInfo()
+    icc_profile = None
+    xmp_data = _extract_xmp_data(exif, verbose, logger)
+    if xmp_data:
+        pnginfo.add_text("XML:com.adobe.xmp", xmp_data)
+        if verbose:
+            logger.info(msg="Added XMP data to PNG info")
+    _add_exif_tags_to_pnginfo(exif, pnginfo, verbose, logger)
+    icc_profile = _extract_icc_profile(exif, verbose, logger)
+    return pnginfo, icc_profile
+
+
+def _extract_xmp_data(exif, verbose, logger):
+    for key, value in exif.items():
+        if isinstance(key, str) and ('xmp' in key.lower() or 'xml' in key.lower()):
+            if isinstance(value, bytes):
+                try:
+                    xmp_data = value.decode('utf-8', errors='ignore')
+                    if verbose:
+                        logger.info(msg=f"Found existing XMP data in source: {key}")
+                    return xmp_data
+                except Exception:
+                    continue
+            elif isinstance(value, str):
+                if verbose:
+                    logger.info(msg=f"Found existing XMP data in source: {key}")
+                return value
+    if verbose:
+        logger.info("Generated new XMP data from EXIF")
+    return create_xmp_from_exif(exif)
+
+
+def _add_exif_tags_to_pnginfo(exif, pnginfo, verbose, logger):
+    for tag_id, value in exif.items():
+        if value is None:
+            continue
+        if isinstance(tag_id, int):
+            _add_exif_tag(pnginfo, tag_id, value, verbose, logger)
+        elif isinstance(tag_id, str) and not tag_id.lower().startswith(('xmp', 'xml')):
+            _add_png_text_tag(pnginfo, tag_id, value, verbose, logger)
+
+
+def _add_exif_tag(pnginfo, tag_id, value, verbose, logger):
+    try:
+        tag_name = TAGS.get(tag_id, f"Unknown_{tag_id}")
+        if isinstance(value, bytes) and len(value) > 1000:
+            return
+        if isinstance(value, (int, float, str)):
+            pnginfo.add_text(tag_name, str(value))
+        elif isinstance(value, bytes):
+            try:
+                decoded_value = value.decode('utf-8', errors='replace')
+                pnginfo.add_text(tag_name, decoded_value)
+            except Exception:
+                pass
+        elif hasattr(value, 'numerator'):  # IFDRational
+            rational_str = f"{value.numerator}/{value.denominator}"
+            pnginfo.add_text(tag_name, rational_str)
+        else:
+            pnginfo.add_text(tag_name, str(value))
+    except Exception as e:
+        if verbose:
+            logger.warning(f"Could not store EXIF tag {tag_id}: {e}")
+
+
+def _add_png_text_tag(pnginfo, key, value, verbose, logger):
+    try:
+        clean_key = key[4:] if key.startswith('PNG_') else key
+        if 'icc' in clean_key.lower() or 'profile' in clean_key.lower():
+            return
+        if isinstance(value, bytes):
+            try:
+                decoded_value = value.decode('utf-8', errors='replace')
+                pnginfo.add_text(clean_key, decoded_value)
+            except Exception:
+                truncated_value = str(value)[:100] + "..."
+                pnginfo.add_text(clean_key, truncated_value)
+        else:
+            pnginfo.add_text(clean_key, str(value))
+    except Exception as e:
+        if verbose:
+            logger.warning(msg=f"Could not store PNG metadata {key}: {e}")
+
+
+def _extract_icc_profile(exif, verbose, logger):
+    for key, value in exif.items():
+        if (isinstance(key, str) and
+            isinstance(value, bytes) and
+                ('icc' in key.lower() or 'profile' in key.lower())):
+            if verbose:
+                logger.info(f"Found ICC profile: {key}")
+            return value
+    return None
+
+
+def _save_png_with_metadata(pil_image, out_filename, pnginfo, icc_profile, verbose, logger):
+    try:
+        save_args = {'format': 'PNG', 'pnginfo': pnginfo}
+        if icc_profile:
+            save_args['icc_profile'] = icc_profile
+            if verbose:
+                logger.info(msg="Saved PNG with ICC profile and metadata")
+        else:
+            if verbose:
+                logger.info(msg="Saved PNG without ICC profile but with metadata")
+        pil_image.save(out_filename, **save_args)
+        if verbose:
+            logger.info(msg=f"Successfully wrote PNG with metadata: {out_filename}")
+    except Exception as e:
+        if verbose:
+            logger.error(msg=f"Failed to write PNG with metadata: {e}")
+            logger.error(traceback.format_exc())
+        pil_image.save(out_filename, format='PNG')
+
+
+def write_image_with_exif_data(exif, image, out_filename, verbose=False, color_order='auto'):
     if exif is None:
         write_img(out_filename, image)
         return None
@@ -168,7 +409,7 @@ def write_image_with_exif_data(exif, image, out_filename, verbose=False):
         tifffile.imwrite(out_filename, image, metadata=metadata, compression='adobe_deflate',
                          extratags=extra_tags, **exif_tags)
     elif extension_png(out_filename):
-        image.save(out_filename, 'PNG', exif=exif, quality=100)
+        write_image_with_exif_data_png(exif, image, out_filename, verbose, color_order=color_order)
     return exif
 
 
@@ -181,8 +422,10 @@ def save_exif_data(exif, in_filename, out_filename=None, verbose=False):
         print_exif(exif)
     if extension_tif(in_filename):
         image_new = tifffile.imread(in_filename)
-    else:
+    elif extension_jpg(in_filename):
         image_new = Image.open(in_filename)
+    elif extension_png(in_filename):
+        image_new = cv2.imread(in_filename, cv2.IMREAD_UNCHANGED)
     if extension_jpg(in_filename):
         add_exif_data_to_jpg_file(exif, in_filename, out_filename, verbose)
     elif extension_tif(in_filename):
@@ -191,7 +434,7 @@ def save_exif_data(exif, in_filename, out_filename=None, verbose=False):
         tifffile.imwrite(out_filename, image_new, metadata=metadata, compression='adobe_deflate',
                          extratags=extra_tags, **exif_tags)
     elif extension_png(in_filename):
-        image_new.save(out_filename, 'PNG', exif=exif, quality=100)
+        write_image_with_exif_data_png(exif, image_new, out_filename, verbose)
     return exif
 
 
@@ -237,4 +480,7 @@ def print_exif(exif, hide_xml=True):
     for tag, (tag_id, data) in exif_data.items():
         if isinstance(data, IFDRational):
             data = f"{data.numerator}/{data.denominator}"
-        logger.info(msg=f"{tag:25} [#{tag_id:5d}]: {data}")
+        if isinstance(tag_id, int):
+            logger.info(msg=f"{tag:25} [#{tag_id:5d}]: {data}")
+        else:
+            logger.info(msg=f"{tag:25} [ {tag_id:20} ]: {str(data)[:100]}...")

shinestacker/algorithms/multilayer.py

@@ -13,7 +13,7 @@ from .. config.constants import constants
 from .. config.config import config
 from .. core.colors import color_str
 from .. core.framework import TaskBase
-from .utils import EXTENSIONS_TIF, EXTENSIONS_JPG, EXTENSIONS_PNG
+from .utils import EXTENSIONS_TIF, EXTENSIONS_JPG, EXTENSIONS_PNG, EXTENSIONS_SUPPORTED
 from .stack_framework import ImageSequenceManager
 from .exif import exif_extra_tags_for_tif, get_exif
 
@@ -142,14 +142,16 @@ def write_multilayer_tiff_from_images(image_dict, output_file, exif_path='', cal
         elif os.path.isdir(exif_path):
             _dirpath, _, fnames = next(os.walk(exif_path))
             fnames = [name for name in fnames
-                      if os.path.splitext(name)[-1][1:].lower() in constants.EXTENSIONS]
-            extra_tags, exif_tags = exif_extra_tags_for_tif(get_exif(exif_path + '/' + fnames[0]))
+                      if os.path.splitext(name)[-1][1:].lower() in EXTENSIONS_SUPPORTED]
+            file_path = os.path.join(exif_path, fnames[0])
+            extra_tags, exif_tags = exif_extra_tags_for_tif(get_exif(file_path))
+        extra_tags = [tag for tag in extra_tags if isinstance(tag[0], int)]
         tiff_tags['extratags'] += extra_tags
         tiff_tags = {**tiff_tags, **exif_tags}
     if callbacks:
         callback = callbacks.get('write_msg', None)
         if callback:
-            callback(output_file.split('/')[-1])
+            callback(os.path.basename(output_file))
     compression = 'adobe_deflate'
     overlayed_images = overlay(
         *((np.concatenate((image, np.expand_dims(transp, axis=-1)),

shinestacker/algorithms/noise_detection.py

@@ -109,13 +109,14 @@ class NoiseDetection(TaskBase, ImageSequenceManager):
                             {'rgb': 'black', 'r': 'red', 'g': 'green', 'b': 'blue'}[ch])
             msg.append(hpx)
         self.print_message(color_str("hot pixels: " + ", ".join(msg), constants.LOG_COLOR_LEVEL_2))
-        path = "/".join(self.file_name.split("/")[:-1])
-        if not os.path.exists(f"{self.working_path}/{path}"):
-            self.print_message(f"create directory: {path}")
-            os.mkdir(f"{self.working_path}/{path}")
-        self.print_message(color_str(f"writing hot pixels map file: {self.file_name}",
+        output_full_path = os.path.join(self.working_path, self.output_path)
+        if not os.path.exists(output_full_path):
+            self.print_message(f"create directory: {self.output_path}")
+            os.mkdir(output_full_path)
+        file_path = os.path.join(self.output_path, self.file_name)
+        self.print_message(color_str(f"writing hot pixels map file: {file_path}",
                                      constants.LOG_COLOR_LEVEL_2))
-        cv2.imwrite(f"{self.working_path}/{self.file_name}", hot_rgb)
+        cv2.imwrite(os.path.join(output_full_path, self.file_name), hot_rgb)
         plot_range = self.plot_range
         min_th, max_th = min(self.channel_thresholds), max(self.channel_thresholds)
         if min_th < plot_range[0]:
@@ -171,8 +172,9 @@ class MaskNoise(SubAction):
         else:
             raise ImageLoadError(path, "file not found.")
 
-    def run_frame(self, _idx, _ref_idx, image):
-        self.process.sub_message_r(color_str(': mask noisy pixels', constants.LOG_COLOR_LEVEL_3))
+    def run_frame(self, idx, _ref_idx, image):
+        self.process.print_message(color_str(
+            f'{self.process.frame_str(idx)}: mask noisy pixels', constants.LOG_COLOR_LEVEL_3))
         shape = image.shape[:2]
         if shape != self.expected_shape:
             raise ShapeError(self.expected_shape, shape)

shinestacker/algorithms/pyramid_tiles.py

@@ -222,7 +222,7 @@ class PyramidTilesStack(PyramidBase):
                         all_level_counts[img_index] = level_count
                         completed_count += 1
                         self.print_message(
-                            f": processing completed, {self.image_str(completed_count - 1)}")
+                            f": preprocessing completed, {self.image_str(completed_count - 1)}")
                     except Exception as e:
                         self.print_message(
                             f"Error processing {self.image_str(i)}: {str(e)}")

shinestacker/algorithms/stack.py

@@ -1,11 +1,13 @@
 # pylint: disable=C0114, C0115, C0116, R0913, R0917
 import os
 import traceback
+import logging
+import numpy as np
 from .. config.constants import constants
 from .. core.framework import TaskBase
 from .. core.colors import color_str
 from .. core.exceptions import InvalidOptionError
-from .utils import write_img, extension_tif_jpg
+from .utils import write_img, extension_supported
 from .stack_framework import ImageSequenceManager, SequentialTask
 from .exif import copy_exif_from_file_to_file
 from .denoise import denoise
@@ -35,18 +37,28 @@ class FocusStackBase(TaskBase, ImageSequenceManager):
             stacked_img = denoise(stacked_img, self.denoise_amount, self.denoise_amount)
         write_img(out_filename, stacked_img)
         if self.exif_path != '':
-            self.sub_message_r(color_str(': copy exif data', constants.LOG_COLOR_LEVEL_3))
-            if not os.path.exists(self.exif_path):
-                raise RuntimeError(f"Path {self.exif_path} does not exist.")
-            try:
-                _dirpath, _, fnames = next(os.walk(self.exif_path))
-                fnames = [name for name in fnames if extension_tif_jpg(name)]
-                exif_filename = os.path.join(self.exif_path, fnames[0])
-                copy_exif_from_file_to_file(exif_filename, out_filename)
-                self.sub_message_r(' ' * 60)
-            except Exception as e:
-                traceback.print_tb(e.__traceback__)
-                raise RuntimeError("Can't copy EXIF data") from e
+            if stacked_img.dtype == np.uint16 and \
+               os.path.splitext(out_filename)[-1].lower() == '.png':
+                self.sub_message_r(color_str(': exif not supported for 16-bit PNG format',
+                                             constants.LOG_COLOR_WARNING),
+                                   level=logging.WARNING)
+            else:
+                self.sub_message_r(color_str(': copy exif data', constants.LOG_COLOR_LEVEL_3))
+                if not os.path.exists(self.exif_path):
+                    raise RuntimeError(f"path {self.exif_path} does not exist.")
+                try:
+                    _dirpath, _, fnames = next(os.walk(self.exif_path))
+                    fnames = [name for name in fnames if extension_supported(name)]
+                    if len(fnames) == 0:
+                        raise RuntimeError(f"path {self.exif_path} does not contain image files.")
+                    exif_filename = os.path.join(self.exif_path, fnames[0])
+                    copy_exif_from_file_to_file(exif_filename, out_filename)
+                    self.sub_message_r(' ' * 60)
+                except Exception as e:
+                    traceback.print_tb(e.__traceback__)
+                    self.sub_message_r(color_str(f': failed to copy EXIF data: {str(e)}',
+                                                 constants.LOG_COLOR_WARNING),
+                                       level=logging.WARNING)
         if self.plot_stack:
             idx_str = f"{self.frame_count + 1:04d}" if self.frame_count >= 0 else ''
             name = f"{self.name}: {self.stack_algo.name()}"

shinestacker/algorithms/stack_framework.py

@@ -7,7 +7,7 @@ from .. core.colors import color_str
 from .. core.framework import Job, SequentialTask
 from .. core.core_utils import check_path_exists
 from .. core.exceptions import RunStopException
-from .utils import read_img, write_img, extension_tif_jpg, get_img_metadata, validate_image
+from .utils import read_img, write_img, extension_supported, get_img_metadata, validate_image
 
 
 class StackJob(Job):
@@ -95,7 +95,7 @@ class ImageSequenceManager:
                 filelist = []
                 for _dirpath, _, filenames in os.walk(d):
                     filelist = [os.path.join(_dirpath, name)
-                                for name in filenames if extension_tif_jpg(name)]
+                                for name in filenames if extension_supported(name)]
                     filelist.sort()
                     if self.reverse_order:
                         filelist.reverse()
@@ -191,7 +191,8 @@ class ImageSequenceManager:
 
 
 class ReferenceFrameTask(SequentialTask, ImageSequenceManager):
-    def __init__(self, name, enabled=True, reference_index=0, step_process=False, **kwargs):
+    def __init__(self, name, enabled=True, reference_index=0,
+                 step_process=constants.DEFAULT_COMBINED_ACTIONS_STEP_PROCESS, **kwargs):
         ImageSequenceManager.__init__(self, name, **kwargs)
         SequentialTask.__init__(self, name, enabled)
         self.ref_idx = reference_index
@@ -276,7 +277,8 @@ class SubAction:
 
 class CombinedActions(ReferenceFrameTask):
     def __init__(self, name, actions=[], enabled=True, **kwargs):
-        ReferenceFrameTask.__init__(self, name, enabled, **kwargs)
+        step_process = kwargs.pop('step_process', constants.DEFAULT_COMBINED_ACTIONS_STEP_PROCESS)
+        ReferenceFrameTask.__init__(self, name, enabled, step_process=step_process, **kwargs)
         self._actions = actions
         self._metadata = (None, None)
 
@@ -294,11 +296,15 @@ class CombinedActions(ReferenceFrameTask):
         self._metadata = get_img_metadata(img)
         return img
 
+    def frame_str(self, idx=-1):
+        if self.run_sequential():
+            idx = self.current_action_count
+        return f"frame {idx + 1}/{self.total_action_counts}"
+
     def run_frame(self, idx, ref_idx):
         input_path = self.input_filepath(idx)
         self.print_message(
-            color_str(f'read input image '
-                      f'{idx + 1}/{self.total_action_counts}, '
+            color_str(f'read input {self.frame_str(idx)}, '
                       f'{os.path.basename(input_path)}', constants.LOG_COLOR_LEVEL_3))
         img = read_img(input_path)
         validate_image(img, *(self._metadata))
@@ -317,20 +323,19 @@ class CombinedActions(ReferenceFrameTask):
                 if img is not None:
                     img = a.run_frame(idx, ref_idx, img)
                 else:
-                    self.sub_message(
-                        color_str(": null input received, action skipped",
+                    self.print_message(
+                        color_str("null input received, action skipped",
                                   constants.LOG_COLOR_ALERT),
                         level=logging.WARNING)
         if img is not None:
             output_path = os.path.join(self.output_full_path(), os.path.basename(input_path))
             self.print_message(
-                color_str(f'write output image '
-                          f'{idx + 1}/{self.total_action_counts}, '
+                color_str(f'write output {self.frame_str(idx)}, '
                           f'{os.path.basename(output_path)}', constants.LOG_COLOR_LEVEL_3))
             write_img(output_path, img)
             return img
         self.print_message(color_str(
-            f"no output file resulted from processing input file: {os.path.basename(input_path)}",
+            f"no output resulted from processing input file: {os.path.basename(input_path)}",
             constants.LOG_COLOR_ALERT), level=logging.WARNING)
         return None
 

shinestacker/algorithms/utils.py

@@ -18,6 +18,15 @@ EXTENSIONS_TIF = ['tif', 'tiff']
 EXTENSIONS_JPG = ['jpg', 'jpeg']
 EXTENSIONS_PNG = ['png']
 EXTENSIONS_PDF = ['pdf']
+EXTENSIONS_SUPPORTED = EXTENSIONS_TIF + EXTENSIONS_JPG + EXTENSIONS_PNG
+EXTENSIONS_GUI_STR = " ".join([f"*.{ext}" for ext in EXTENSIONS_SUPPORTED])
+EXTENSION_GUI_TIF = " ".join([f"*.{ext}" for ext in EXTENSIONS_TIF])
+EXTENSION_GUI_JPG = " ".join([f"*.{ext}" for ext in EXTENSIONS_JPG])
+EXTENSION_GUI_PNG = " ".join([f"*.{ext}" for ext in EXTENSIONS_PNG])
+EXTENSIONS_GUI_SAVE_STR = f"TIFF Files ({EXTENSION_GUI_TIF});;" \
+                          f"JPEG Files ({EXTENSION_GUI_JPG});;" \
+                          f"PNG Files ({EXTENSION_GUI_PNG});;" \
+                          "All Files (*)"
 
 
 def extension_in(path, exts):
@@ -56,6 +65,10 @@ def extension_jpg_tif_png(path):
     return extension_in(path, EXTENSIONS_JPG + EXTENSIONS_TIF + EXTENSIONS_PNG)
 
 
+def extension_supported(path):
+    return extension_in(path, EXTENSIONS_SUPPORTED)
+
+
 def read_img(file_path):
     if not os.path.isfile(file_path):
         raise RuntimeError("File does not exist: " + file_path)
@@ -73,7 +86,10 @@ def write_img(file_path, img):
     elif extension_tif(file_path):
         cv2.imwrite(file_path, img, [int(cv2.IMWRITE_TIFF_COMPRESSION), 1])
     elif extension_png(file_path):
-        cv2.imwrite(file_path, img)
+        cv2.imwrite(file_path, img, [
+            int(cv2.IMWRITE_PNG_COMPRESSION), 9,
+            int(cv2.IMWRITE_PNG_STRATEGY), cv2.IMWRITE_PNG_STRATEGY_HUFFMAN_ONLY
+        ])
 
 
 def img_8bit(img):
@@ -96,7 +112,7 @@ def img_bw(img):
 def get_first_image_file(filenames):
     first_img_file = None
     for filename in filenames:
-        if os.path.isfile(filename) and extension_tif_jpg(filename):
+        if os.path.isfile(filename) and extension_supported(filename):
             first_img_file = filename
             break
     if first_img_file is None:

shinestacker/algorithms/vignetting.py

@@ -4,7 +4,7 @@ import traceback
 import logging
 import numpy as np
 import matplotlib.pyplot as plt
-from scipy.optimize import curve_fit, fsolve
+from scipy.optimize import curve_fit, bisect
 import cv2
 from .. core.colors import color_str
 from .. core.core_utils import setup_matplotlib_mode
@@ -181,9 +181,22 @@ class Vignetting(SubAction):
             self.process.callback(
                 constants.CALLBACK_SAVE_PLOT, self.process.id,
                 f"{self.process.name}: intensity\nframe {idx_str}", plot_path)
+
         for i, p in enumerate(self.percentiles):
-            self.corrections[i][idx] = fsolve(lambda x: sigmoid_model(x, *params) /
-                                              self.v0 - p, r0_fit)[0]
+            s1 = sigmoid_model(0, *params) / self.v0
+            s2 = sigmoid_model(self.r_max, *params) / self.v0
+            if s1 > p > s2:
+                try:
+                    c = bisect(lambda x: sigmoid_model(x, *params) / self.v0 - p, 0, self.r_max)
+                except Exception as e:
+                    traceback.print_tb(e.__traceback__)
+                    self.process.sub_message(color_str(f": {str(e).lower()}", "yellow"),
+                                             level=logging.WARNING)
+            elif s1 <= p:
+                c = 0
+            else:
+                c = self.r_max
+            self.corrections[i][idx] = c
         self.process.print_message(
             color_str(f"{self.process.idx_tot_str(idx)}: correct vignetting", "cyan"))
         return correct_vignetting(