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Make annotation font size configurable
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@kochanczyk
kochanczyk committed Aug 29, 2024
1 parent cbf19a5 commit c271114
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5 changes: 5 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -193,6 +193,11 @@ Remixes:
```
(an immunostaining from 2024-04-04 by Juan Alfonso Redondo Marin).

The four sections above are obligatory. You may also include optional sections:
```
Annotations:
font_size: 32pt # default is 96pt
```


Inspection
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57 changes: 37 additions & 20 deletions maestro.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,8 @@
FIJI_EXE_PATH = Path('/opt/fiji/Fiji.app/ImageJ-linux64')
FIJI_SCRIPT_BASE_PATH = Path('/tmp/stitch-')

TEXT_ANNOTATIONS_DEFAULT_FONT_SIZE = 96

FFMPEG_EXE_PATH = Path('/usr/bin/ffmpeg')
FFMPEG_OPTS_SILENCE = '-nostdin -loglevel error -y'.split()
FFMPEG_OPTS_CODEC = '-vcodec libx264 -pix_fmt yuv420p -an'.split() # -b:v 24M
Expand Down Expand Up @@ -435,7 +437,7 @@ def stitch_tiles(
zero_pixels_in_output_image_retries_count = 0


desc = f"[{well_id}] {STITCHES_FOLDER_BASE_NAME}: fijing: "
desc = f"[{well_id}] {STITCHES_FOLDER_BASE_NAME}: {'fijing:' if n_fields_x*n_fields_y>1 else 'copying:'}"
for timepoint, tile_images_paths in tqdm(tile_images_paths_grouped_by_timepoint, desc=desc,
**TQDM_STYLE):

Expand All @@ -453,7 +455,6 @@ def stitch_tiles(

else:


n_trials_remaining = zero_pixels_in_output_image_retries_count
zero_pixel_counts = []
while n_trials_remaining > 0:
Expand Down Expand Up @@ -492,6 +493,7 @@ def stitch_tiles(
sp.run(cmd, stdout=sp.DEVNULL, stderr=sp.DEVNULL, check=True, timeout=3600)
except sp.TimeoutExpired:
print('Fiji TIMED OUT while stitching!')
raise
except:
with open(fiji_script_path_s, 'r', encoding='utf-8') as f:
print(40*'- ')
Expand All @@ -513,12 +515,10 @@ def stitch_tiles(
break
continue # retry

if compress_output_tif:
dst_file_path_s = str(dst_file_path.absolute())
cmd = [CONVERT_EXE_PATH_S, dst_file_path_s, '-compress', 'zip', dst_file_path_s]
sp.run(cmd, stdout=sp.DEVNULL, stderr=sp.DEVNULL, check=True)

break
if compress_output_tif:
dst_file_path_s = str(dst_file_path.absolute())
cmd = [CONVERT_EXE_PATH_S, dst_file_path_s, '-compress', 'zip', dst_file_path_s]
sp.run(cmd, stdout=sp.DEVNULL, stderr=sp.DEVNULL, check=True)



Expand Down Expand Up @@ -614,6 +614,7 @@ def remix_channels(
force: bool = False,
wells_info_for_annotation: pd.DataFrame | None = None,
is_part_of_timeseries: bool = False,
annotation_font_size: int = TEXT_ANNOTATIONS_DEFAULT_FONT_SIZE,
) -> None:

assert stitches_folder_path.exists() and stitches_folder_path.is_dir()
Expand Down Expand Up @@ -728,19 +729,19 @@ def remix_channels(
cmd = [
'convert',
'-size', '1800x1200+0+0', 'xc:none',
'-font', 'Helvetica', '-pointsize', '96',
'-font', 'Helvetica', '-pointsize', str(annotation_font_size),
'-stroke', 'gray', '-strokewidth', '2',
'-gravity', 'north-west',
'-annotate', '0', text,
'-background', 'none',
'-shadow', '1800x0+0+0', '+repage',
'-font', 'Helvetica', '-pointsize', '96',
'-font', 'Helvetica', '-pointsize', str(annotation_font_size),
'-stroke', 'none', '-fill', 'LightGray',
'-gravity', 'north-west',
'-annotate', '0', text,
target_image_path_s, '+swap',
'-gravity', 'north-west',
'-geometry', '+24+24',
'-geometry', f"+{annotation_font_size//4}+{annotation_font_size//4}",
'-composite',
target_image_path_s,
]
Expand All @@ -755,6 +756,7 @@ def _annotate_remixes_with_timestamps(
delta_t_secs: float,
obs_suffix: str,
force: bool = False,
annotation_font_size: int = TEXT_ANNOTATIONS_DEFAULT_FONT_SIZE,
) -> None:

remixes_image_files_paths = well_remixes_folder_path.glob(f"Img_t*--{obs_suffix}.png")
Expand All @@ -772,17 +774,17 @@ def _annotate_remixes_with_timestamps(
'convert',
'-size', '360x90', 'xc:none',
'-gravity', 'center',
'-font', 'Helvetica', '-pointsize', '96',
'-font', 'Helvetica', '-pointsize', str(annotation_font_size),
'-stroke', 'gray', '-strokewidth', '2',
'-annotate', '0', time_min_s,
'-background', 'none',
'-shadow', '360x5+0+0', '+repage',
'-font', 'Helvetica', '-pointsize', '96',
'-font', 'Helvetica', '-pointsize', str(annotation_font_size),
'-stroke', 'none', '-fill', 'LightGray',
'-annotate', '0', time_min_s,
str(path.absolute()), '+swap',
'-gravity', 'north-west',
'-geometry', '+40+24',
'-geometry', f"+{annotation_font_size//2}+{annotation_font_size//4}",
'-composite',
str(p_annot.absolute())
]
Expand Down Expand Up @@ -846,6 +848,7 @@ def encode_movies(
well_movies_folder_path: Path,
force: bool = False,
annotate_with_timestamp: bool = True,
annotation_font_size: int = TEXT_ANNOTATIONS_DEFAULT_FONT_SIZE,
force_annotation: bool = False,
clean_up_images_annotated_with_timestamp: bool = True,
apply_stabilization: bool = False,
Expand All @@ -854,7 +857,7 @@ def encode_movies(

assert delta_t is not None
delta_t_secs = delta_t.total_seconds()
movie_fps_s = f"3600/{round(delta_t_secs)}" # rational; so that 1h of movie ~ 1m of experiment
movie_fps_s = f"3600/{round(delta_t_secs)}" # rational
movie_fps_i = round(3600/delta_t_secs) # used for frequency of keyint insertion
movie_fps_i = max(movie_fps_i, 1)

Expand All @@ -873,7 +876,8 @@ def encode_movies(
if annotate_with_timestamp:
_annotate_remixes_with_timestamps(well_id, well_remixes_folder_path,
well_movies_folder_path, delta_t_secs, obs_suffix,
force=force_annotation)
force=force_annotation,
annotation_font_size=annotation_font_size)
source_image_files_folder_path = well_movies_folder_path
input_image_filename_pattern = f"Img_t%04d--{obs_suffix}{TIMESTAMP_SUFFIX}.png"
else:
Expand Down Expand Up @@ -1443,6 +1447,9 @@ def remaster(
config_file_path = Path(config_file)
with open(config_file_path, 'r', encoding='UTF-8') as config_file_io:
config = yaml.load(config_file_io, Loader=yaml.FullLoader)
for obligatory_section in ('Observables', 'Normalization', 'Stitching', 'Remixes'):
assert obligatory_section in config, \
f"Error: Section '{obligatory_section}' missing in the config file."

# output folder
output_folder_path = Path(output_folder)
Expand Down Expand Up @@ -1470,7 +1477,6 @@ def remaster(
wells_info_str = wells_info.to_string(max_cols=100)
print(80*'-' + '\n', wells_info_str, '\n' + 80*'-')


channels_info['Observable'] = channels_info['Name'].map(config['Observables'])
missing_observables = channels_info[ channels_info['Observable'].isna() ]['Name']
assert len(missing_observables) == 0, \
Expand Down Expand Up @@ -1504,6 +1510,14 @@ def remaster(
remixing_downscale = config['Remixes']['downscale'] \
if 'downscale' in config['Remixes'] else False

# text annotation settings
if 'Annotations' in config and 'font_size' in config['Annotations']:
annotation_font_size = int(config['Annotations']['font_size'].replace('pt', ''))
else:
annotation_font_size = TEXT_ANNOTATIONS_DEFAULT_FONT_SIZE
print(f"Info: Assumed default text annotation font size: {TEXT_ANNOTATIONS_DEFAULT_FONT_SIZE} pt.")


# selection of wells
if well is not None:
is_re = len(set(well).intersection(set('*.[{?^'))) > 0
Expand Down Expand Up @@ -1626,7 +1640,8 @@ def remaster(
force=force_remix,
wells_info_for_annotation = \
wells_info if annotate_remixes_with_wells_info else None,
is_part_of_timeseries=n_timepoints > 1
is_part_of_timeseries=n_timepoints > 1,
annotation_font_size=annotation_font_size,
)


Expand Down Expand Up @@ -1670,7 +1685,8 @@ def remaster(
force=force_remix,
wells_info_for_annotation = \
wells_info if annotate_remixes_with_wells_info else None,
is_part_of_timeseries=n_timepoints > 1
is_part_of_timeseries=n_timepoints > 1,
annotation_font_size=annotation_font_size,
)


Expand All @@ -1694,7 +1710,8 @@ def remaster(
time_interval,
well_remixes_folder_path,
well_movies_folder_path,
force=force_encode
force=force_encode,
annotation_font_size=annotation_font_size,
)
else:
print(f"[{well_id}] (encoding of movies skipped)")
Expand Down

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