Skip to content

Commit

Permalink
Merge branch 'main' of https://github.com/EtalumaSupport/LumaViewPro
Browse files Browse the repository at this point in the history
  • Loading branch information
@dovydasv2
dovydasv2 committed Nov 7, 2024
2 parents 2f84c55 + 2fb9a9f commit 6739c2c
Show file tree
Hide file tree
Showing 7 changed files with 298 additions and 74 deletions.
291 changes: 233 additions & 58 deletions image_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,29 @@

import modules.common_utils as common_utils
import image_utils

from lvp_logger import logger

import datetime
from fractions import Fraction

from lvp_logger import logger, version

# Conversion to tifffile's desired datatype references
tifffile_dtypes = {
'BYTE': 1,
'ASCII': 2,
'SHORT': 3,
'LONG': 4,
'RATIONAL': 5,
'SBYTE': 6,
'UNDEFINED': 7,
'SSHORT': 8,
'SLONG': 9,
'SRATIONAL': 10,
'FLOAT': 11,
'DOUBLE': 12,
'SINGLE': 13,
'QWORD': 16,
'SQWORD': 17,
}

def is_color_image(image) -> bool:
if len(image.shape) == 3 and image.shape[2] == 3:
Expand Down Expand Up @@ -114,7 +134,54 @@ def convert_16bit_to_8bit(image):
return (new_image/256).astype('uint8')


def generate_ome_tiff_support_data(data, metadata: dict):
def write_tiff(
data,
file_loc: pathlib.Path,
metadata: dict,
ome: bool,
video_frame: bool = False,
extratags: list = [],
):

# Note: OpenCV and TIFFFILE have the Red/Blue color planes swapped, so need to swap
# them before writing out to tiff
use_color = image_utils.is_color_image(data)
if use_color:
data = cv2.cvtColor(data, cv2.COLOR_BGR2RGB)

support_data = generate_tiff_data(data=data, metadata=metadata, ome=ome, video_frame=video_frame)

if True == ome:
kwargs = {
'bigtiff': False
}
else:
kwargs = {}

with tf.TiffWriter(str(file_loc), **kwargs) as tif:
if not video_frame:
tif.write(
data,
resolution=support_data['resolution'],
metadata=support_data['metadata'],
datetime=metadata['datetime'],
software=f"LumaViewPro {version}",
**support_data['options'],
)
else:
tif.write(
data,
metadata=support_data['metadata'],
datetime=metadata['datetime'],
software=f"LumaViewPro {version}",
**support_data['options'],
)


def generate_tiff_data(data, metadata: dict, ome: bool, video_frame: bool):

dtype = tifffile_dtypes

use_color = image_utils.is_color_image(data)

if use_color:
Expand All @@ -124,29 +191,145 @@ def generate_ome_tiff_support_data(data, metadata: dict):
photometric = 'minisblack'
axes = 'YX'

ome_metadata={
'axes': axes,
'SignificantBits': data.itemsize*8,
'PhysicalSizeX': metadata['pixel_size_um'],
'PhysicalSizeXUnit': 'µm',
'PhysicalSizeY': metadata['pixel_size_um'],
'PhysicalSizeYUnit': 'µm',
'Channel': {'Name': [metadata['channel']]},
'Plane': {
'PositionX': metadata['plate_pos_mm']['x'],
'PositionY': metadata['plate_pos_mm']['y'],
'PositionZ': metadata['z_pos_um'],
'PositionXUnit': 'mm',
'PositionYUnit': 'mm',
'PositionZUnit': 'um',
'ExposureTime': metadata['exposure_time_ms'],
'ExposureTimeUnit': 'ms',
'Gain': metadata['gain_db'],
'GainUnit': 'dB',
'Illumination': metadata['illumination_ma'],
'IlluminationUnit': 'mA'
"""
To Add:
ImageNumber
LensModel
"""
if True == ome:
tiff_metadata={
'axes': axes,
'SignificantBits': data.itemsize*8,
'PhysicalSizeX': metadata['pixel_size_um'],
'PhysicalSizeXUnit': 'µm',
'PhysicalSizeY': metadata['pixel_size_um'],
'PhysicalSizeYUnit': 'µm',
'Channel': {'Name': [metadata['channel']]},
'Plane': {
'PositionX': metadata['plate_pos_mm']['x'],
'PositionY': metadata['plate_pos_mm']['y'],
'PositionZ': metadata['z_pos_um'],
'PositionXUnit': 'mm',
'PositionYUnit': 'mm',
'PositionZUnit': 'um',
'ExposureTime': metadata['exposure_time_ms'],
'ExposureTimeUnit': 'ms',
'Gain': metadata['gain_db'],
'GainUnit': 'dB',
'Illumination': metadata['illumination_ma'],
'IlluminationUnit': 'mA'
}
}
}
tiff_extratags = []
# Metadata seems to be working properly for OME-TIFF's so let's leave it alone for now.

else:
if not video_frame:
tiff_metadata={
"CameraMake": metadata['camera_make'],
"ExposureTime": metadata['exposure_time_ms'],
"ISOSpeed": metadata['gain_db'],
"DateTime": metadata['datetime'],
"Software": metadata['software'],
"XPosition": metadata['x_pos'],
"YPosition": metadata['y_pos'],
"SubjectDistance": metadata['z_pos_um'],
"SubSecTime": metadata['sub_sec_time'],
"Channel": metadata['channel'],
"BrightnessValue": metadata['illumination_ma']
}
# extratags:
# Additional tags to write. A list of tuples with 5 items:
#
# 0. code (int): Tag Id.
#
# 1. dtype (:py:class:`DATATYPE`):
# Data type of items in `value`.
#
# 2. count (int): Number of data values.
# Not used for string or bytes values.
#
# 3. value (Sequence[Any]): `count` values compatible with
# `dtype`. Bytes must contain count values of dtype packed
# as binary data.
#
# 4. writeonce (bool): If *True*, write tag to first page
# of a series only.
#
# Duplicate and select tags in TIFF.TAG_FILTERED are not written
# if the extratag is specified by integer code.
#
# Extratags cannot be used to write IFD type tags.
#
# Format: (tag_number, datatype, count, value, write_ifd)
# For rational number values: (numerator, denominator)
tiff_extratags = []
"""tiff_extratags = [
# CameraMake: Tag ID 271, 'ASCII'
(271, dtype['ASCII'], len(metadata['camera_make']) + 1, metadata['camera_make'], False),
# ExposureTime: Tag ID 33434, 'RATIONAL'
(33434, dtype['RATIONAL'], 1, ms_exposure_to_rational(metadata['exposure_time_ms']), False),
# ISOSpeed: Tag ID 34867, 'double'
# Using in place of GainControl (Improper use of GainControl)
(34867, dtype['DOUBLE'], 1, metadata['gain_db'], False),
# DateTime: Tag ID 306, 'ASCII'
(306, dtype['ASCII'], len(metadata['datetime']) + 1, metadata['datetime'], False),
# SubjectDistance: Tag ID 37386, 'RATIONAL'
(37386, dtype['RATIONAL'], 1, subject_dist_to_rational(metadata['z_pos_um']), False),
# SubSecTime: Tag ID 37520, 'ASCII'
(37520, dtype['ASCII'], len(metadata['sub_sec_time']) + 1, metadata['sub_sec_time'], False),
# Channel: Tag ID 65001, 'ASCII' **CUSTOM**
(65001, dtype['ASCII'], len(metadata['channel']) + 1, metadata['channel'], False),
# BrightnessValue: Tag ID 37393, 'SRATIONAL'
(37393, dtype['SRATIONAL'], 1, (metadata['illumination_ma'], 1), False)]"""

"""
# XPosition: Tag ID 65001, 'RATIONAL'
# Need to double check units
(286, dtype['RATIONAL'], 1, (metadata['x_pos'], 1), False),]
# YPosition: Custom Tag ID 65002, 'RATIONAL'
# Need to double check units
(287, dtype['RATIONAL'], 1, (metadata['y_pos'], 1), False),
"""



else:
# Video Frame
# Add further parameters in the future if testing goes well

"""date_time_data = metadata['timestamp'].strftime("%Y:%m:%d %H:%M:%S")
sub_sec_time = f"{metadata['timestamp'].microsecond // 1000:03d}"
tiff_extratags = [
# Tag 306: DateTime (ASCII)
(306, 'ascii', len(date_time_data) + 1, date_time_data, False),
# Tag 37520: SubSecTime (ASCII)
(37520, 'ascii', len(sub_sec_time) + 1, sub_sec_time, False),
# Tag 37393: ImageNumber (long)
(37393, 'long', 1, metadata['frame_num'], False)
]"""
tiff_extratags = []
tiff_metadata = metadata



options=dict(
photometric=photometric,
Expand All @@ -156,41 +339,33 @@ def generate_ome_tiff_support_data(data, metadata: dict):
maxworkers=2
)

resolution = (1e4 / metadata['pixel_size_um'], 1e4 / metadata['pixel_size_um'])

return {
'metadata': ome_metadata,
'options': options,
'resolution': resolution,
}
if not video_frame:
resolution = (1e4 / metadata['pixel_size_um'], 1e4 / metadata['pixel_size_um'])

return {
'metadata': tiff_metadata,
'extratags': tiff_extratags,
'options': options,
'resolution': resolution,
}

else:
return {
'metadata': tiff_metadata,
'extratags': tiff_extratags,
'options': options,
}

def write_ome_tiff(
data,
file_loc: pathlib.Path,
metadata: dict,
):
# Note: OpenCV and TIFFFILE have the Red/Blue color planes swapped, so need to swap
# them before writing out to OME tiff
use_color = image_utils.is_color_image(data)
if use_color:
data = cv2.cvtColor(data, cv2.COLOR_BGR2RGB)
def ms_exposure_to_rational(ms_exposure):
exposure_seconds = ms_exposure / 1000
fraction = Fraction(exposure_seconds).limit_denominator(1_000_000)
# Metadata uses rational number of seconds
return fraction.numerator, fraction.denominator

# if use_color:
# photometric = 'rgb'
# axes = 'YXS'
# else:
# photometric = 'minisblack'
# axes = 'YX'
ome_tiff_support_data = generate_ome_tiff_support_data(data=data, metadata=metadata)

with tf.TiffWriter(str(file_loc), bigtiff=False) as tif:
tif.write(
data,
resolution=ome_tiff_support_data['resolution'],
metadata=ome_tiff_support_data['metadata'],
**ome_tiff_support_data['options']
)
def subject_dist_to_rational(distance):
distance_meters = distance / 1_000_000 # Convert um to m
fraction = Fraction(distance_meters).limit_denominator(1_000_000)
return fraction.numerator, fraction.denominator


def add_scale_bar(
Expand Down
27 changes: 18 additions & 9 deletions lumascope_api.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@
from pyloncamera import PylonCamera

# Import additional libraries
from lvp_logger import logger
from lvp_logger import logger, version
import modules.common_utils as common_utils
import modules.coord_transformations as coord_transformations
import modules.objectives_loader as objectives_loader
Expand Down Expand Up @@ -398,9 +398,15 @@ def _validate():
)

metadata = {
'camera_make': 'Etaluma',
'software': f'LumaViewPro {version}',
'channel': color,
'datetime': datetime.datetime.now().strftime("%Y:%m:%d %H:%M:%S"), # Format for metadata
'sub_sec_time': f"{datetime.datetime.now().microsecond // 1000:03d}",
'focal_length': self._objective['focal_length'],
'plate_pos_mm': {'x': px, 'y': py},
'x_pos': px,
'y_pos': py,
'z_pos_um': z,
'exposure_time_ms': round(self.get_exposure_time(), common_utils.max_decimal_precision('exposure')),
'gain_db': round(self.get_gain(), common_utils.max_decimal_precision('gain')),
Expand Down Expand Up @@ -476,15 +482,18 @@ def save_image(
metadata = image_data['metadata']
file_loc = metadata['file_loc']

if output_format == 'OME-TIFF':
ome=True
else:
ome=False

try:
if output_format == 'OME-TIFF':
image_utils.write_ome_tiff(
data=image,
file_loc=file_loc,
metadata=metadata,
)
else:
cv2.imwrite(str(file_loc), image.astype(array.dtype))
image_utils.write_tiff(
data=image,
file_loc=file_loc,
metadata=metadata,
ome=ome,
)

logger.info(f'[SCOPE API ] Saving Image to {file_loc}')
except:
Expand Down
18 changes: 16 additions & 2 deletions lumaviewpro.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1328,8 +1328,22 @@ def recording_complete(self, dt):

output_file_loc = save_folder / f"{frame_name}.tiff"

if not cv2.imwrite(filename=str(output_file_loc), img=image):
logger.error(f"Manual-Video] Failed to write frame {frame_num}")
metadata = {
"datetime": ts.strftime("%Y:%m:%d %H:%M:%S"),
"timestamp": ts.strftime("%Y:%m:%d %H:%M:%S.%f"),
"frame_num": frame_num
}

try:
image_utils.write_tiff(
data=image,
metadata=metadata,
file_loc=output_file_loc,
video_frame=True,
ome=False,
)
except Exception as e:
logger.error(f"Protocol-Video] Failed to write frame {frame_num}: {e}")

else:
if not self.video_save_folder.exists():
Expand Down
Loading

0 comments on commit 6739c2c

Please sign in to comment.