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Fix converter for ndtiff using multicam #218

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Fix converter for ndtiff using multicam #218

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15 changes: 12 additions & 3 deletions iohub/convert.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -147,6 +147,7 @@ def __init__(
# for `get_num_positions()`
self.p = self.reader.num_positions
self.t = self.reader.frames
self.cams = self.reader.cameras # multicam
self.c = self.reader.channels
self.z = self.reader.slices
self.y = self.reader.height
Expand Down Expand Up @@ -474,7 +475,7 @@ def _convert_ndtiff(self):
)
try:
ndtiff_pos_idx, *_ = self.reader._check_coordinates(
ndtiff_pos_idx, 0, 0, 0
ndtiff_pos_idx, 0, 0, 0, 0
)
except ValueError:
# Log warning and continue if some positions were not
Expand All @@ -489,13 +490,18 @@ def _convert_ndtiff(self):
zarr_pos_name = self.zarr_position_names[p_idx]
zarr_arr = self.writer[zarr_pos_name]["0"]

for t_idx, c_idx in product(
for t_idx, c_idx, cam_idx in product(
range(self.t),
range(self.c),
range(len(self.cams)),
bar_format=bar_format_time_channel,
position=1,
leave=False,
):
if self.reader.cameras is not None:
c_idx = c_idx // len(self.cams)
ndtiff_cam_str = self.reader.cameras[cam_idx]

ndtiff_channel_idx = (
self.reader.channel_names[c_idx]
if self.reader.str_channel_axis
Expand All @@ -507,9 +513,10 @@ def _convert_ndtiff(self):
_,
ndtiff_t_idx,
ndtiff_channel_idx,
ndtiff_cam_str,
ndtiff_z_idx,
) = self.reader._check_coordinates(
ndtiff_pos_idx, t_idx, ndtiff_channel_idx, 0
ndtiff_pos_idx, t_idx, ndtiff_channel_idx, 0, 0
)
# Log warning and continue if some T/C were not acquired in the
# dataset
Expand All @@ -518,6 +525,7 @@ def _convert_ndtiff(self):
time=ndtiff_t_idx,
channel=ndtiff_channel_idx,
z=ndtiff_z_idx,
camera=ndtiff_cam_str,
):
logging.warning(
f"Cannot load data at timepoint {t_idx}, channel "
Expand All @@ -540,6 +548,7 @@ def _convert_ndtiff(self):
ndtiff_pos_idx,
ndtiff_t_idx,
ndtiff_channel_idx,
ndtiff_cam_str,
z_idx,
)
# T/C/Z
Expand Down
73 changes: 57 additions & 16 deletions iohub/ndtiff.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,10 +23,14 @@ def __init__(self, data_path: str):
self.frames = (
len(self._axes["time"]) if "time" in self._axes.keys() else 1
)
self.slices = len(self._axes["z"]) if "z" in self._axes.keys() else 1
self.cameras = (
self._axes["camera"] if "camera" in self._axes.keys() else []
)
self.channels = (
len(self._axes["channel"]) if "channel" in self._axes.keys() else 1
)
self.slices = len(self._axes["z"]) if "z" in self._axes.keys() else 1

self.height = self.dataset.image_height
self.width = self.dataset.image_width
self.dtype = self.dataset.dtype
Expand All @@ -37,20 +41,29 @@ def __init__(self, data_path: str):
self.z_step_size = self.mm_meta["Summary"]["z-step_um"]
self.xy_pixel_size = self.mm_meta["Summary"].get("PixelSize_um", 1.0)

if len(self.cameras) > 1:
channel_names = []
self.channels = self.channels * len(self.cameras)
for chan_name in self.channel_names:
for cam in self.cameras:
channel_names.append(chan_name + "_" + cam)
self.channel_names = channel_names

def _get_summary_metadata(self):
pm_metadata = self.dataset.summary_metadata
pm_metadata["MicroManagerVersion"] = "pycromanager"
pm_metadata["Positions"] = self.get_num_positions()
img_metadata = self.get_image_metadata(0, 0, 0, 0)

img_metadata = self.get_image_metadata(0, 0, 0, 0, 0)

pm_metadata["z-step_um"] = None
if "ZPosition_um_Intended" in img_metadata.keys():
pm_metadata["z-step_um"] = np.around(
abs(
self.get_image_metadata(0, 0, 0, 1)[
self.get_image_metadata(0, 0, 0, 0, 1)[
"ZPosition_um_Intended"
]
- self.get_image_metadata(0, 0, 0, 0)[
- self.get_image_metadata(0, 0, 0, 0, 0)[
"ZPosition_um_Intended"
]
),
Expand All @@ -61,7 +74,7 @@ def _get_summary_metadata(self):
if "position" in self._axes:
for position in self._axes["position"]:
position_metadata = {}
img_metadata = self.get_image_metadata(position, 0, 0, 0)
img_metadata = self.get_image_metadata(position, 0, 0, 0, 0)

if img_metadata is not None and all(
key in img_metadata.keys()
Expand Down Expand Up @@ -102,15 +115,20 @@ def str_channel_axis(self) -> bool:
return self._str_channel_axis

def _check_coordinates(
self, p: Union[int, str], t: int, c: Union[int, str], z: int
self,
p: Union[int, str],
t: int,
c: Union[int, str],
camera: Union[int, str],
z: int,
):
"""
Check that the (p, t, c, z) coordinates are part of the ndtiff dataset.
Replace coordinates with None or string values in specific cases - see
below
"""
coords = [p, t, c, z]
axes = ("position", "time", "channel", "z")
coords = [p, t, c, camera, z]
axes = ("position", "time", "channel", "camera", "z")

for i, axis in enumerate(axes):
coord = coords[i]
Expand Down Expand Up @@ -172,7 +190,12 @@ def get_num_positions(self) -> int:
)

def get_image(
self, p: Union[int, str], t: int, c: Union[int, str], z: int
self,
p: Union[int, str],
t: int,
c: Union[int, str],
camera: Union[int, str],
z: int,
) -> np.ndarray:
"""return the image at the provided PTCZ coordinates

Expand All @@ -194,10 +217,20 @@ def get_image(
"""

image = None
p, t, c, z = self._check_coordinates(p, t, c, z)
p, t, c, camera, z = self._check_coordinates(
p,
t,
c,
camera,
z,
)

if self.dataset.has_image(position=p, time=t, channel=c, z=z):
image = self.dataset.read_image(position=p, time=t, channel=c, z=z)
if self.dataset.has_image(
position=p, time=t, channel=c, camera=camera, z=z
):
image = self.dataset.read_image(
position=p, time=t, channel=c, camera=camera, z=z
)

return image

Expand Down Expand Up @@ -238,6 +271,7 @@ def get_zarr(self, position: Union[int, str]) -> zarr.array:
position = None

da = self.dataset.as_array(position=position)

shape = (
self.frames,
self.channels,
Expand Down Expand Up @@ -265,7 +299,12 @@ def get_array(self, position: Union[int, str]) -> np.ndarray:
return np.asarray(self.get_zarr(position))

def get_image_metadata(
self, p: Union[int, str], t: int, c: Union[int, str], z: int
self,
p: Union[int, str],
t: int,
c: Union[int, str],
z: int,
camera: Union[int, str],
) -> dict:
"""Return image plane metadata at the requested PTCZ coordinates

Expand All @@ -286,11 +325,13 @@ def get_image_metadata(
image plane metadata
"""
metadata = None
p, t, c, z = self._check_coordinates(p, t, c, z)
p, t, c, camera, z = self._check_coordinates(p, t, c, z, camera)

if self.dataset.has_image(position=p, time=t, channel=c, z=z):
if self.dataset.has_image(
position=p, time=t, channel=c, z=z, camera=camera
):
metadata = self.dataset.read_metadata(
position=p, time=t, channel=c, z=z
position=p, time=t, channel=c, z=z, camera=camera
)

return metadata