error loading new video

[leodiej]

Hello,
I am trying to perform the code with a tiff video. The file's name is "video conversion .tiff". Here is the code I ran and the error I get.

Set up Initial Basic Parameters#

minian_path = "."
dpath = "./inscopix_video/"
minian_ds_path = os.path.join(dpath, "minian")
intpath = "./fichier_intermediaire"
subset = dict(frame=slice(0, None))
subset_mc = None
interactive = True
output_size = 100
n_workers = int(os.getenv("MINIAN_NWORKERS", 4))
param_save_minian = {
"dpath": minian_ds_path,
"meta_dict": dict(session=-1, animal=-2),
"overwrite": True,
}

Pre-processing Parameters#

param_load_videos = {
"pattern": "video conversion[0].tiff",
"dtype": np.uint8,
"downsample": dict(frame=1, height=1, width=1),
"downsample_strategy": "subset",
}
param_denoise = {"method": "median", "ksize": 7}
param_background_removal = {"method": "tophat", "wnd": 15}

Motion Correction Parameters#

subset_mc = None
param_estimate_motion = {"dim": "frame"}

Initialization Parameters#

param_seeds_init = {
"wnd_size": 1000,
"method": "rolling",
"stp_size": 500,
"max_wnd": 15,
"diff_thres": 3,
}
param_pnr_refine = {"noise_freq": 0.06, "thres": 1}
param_ks_refine = {"sig": 0.05}
param_seeds_merge = {"thres_dist": 10, "thres_corr": 0.8, "noise_freq": 0.06}
param_initialize = {"thres_corr": 0.8, "wnd": 10, "noise_freq": 0.06}
param_init_merge = {"thres_corr": 0.8}

CNMF Parameters#

param_get_noise = {"noise_range": (0.06, 0.5)}
param_first_spatial = {
"dl_wnd": 10,
"sparse_penal": 0.01,
"size_thres": (25, None),
}
param_first_temporal = {
"noise_freq": 0.06,
"sparse_penal": 1,
"p": 1,
"add_lag": 20,
"jac_thres": 0.2,
}
param_first_merge = {"thres_corr": 0.8}
param_second_spatial = {
"dl_wnd": 10,
"sparse_penal": 0.01,
"size_thres": (25, None),
}
param_second_temporal = {
"noise_freq": 0.06,
"sparse_penal": 1,
"p": 1,
"add_lag": 20,
"jac_thres": 0.4,
}

os.environ["OMP_NUM_THREADS"] = "1"
os.environ["MKL_NUM_THREADS"] = "1"
os.environ["OPENBLAS_NUM_THREADS"] = "1"
os.environ["fichier_intermediaire"] = intpath

The error is coming after this cell:

varr = load_videos(dpath, **param_load_videos)
chk, _ = get_optimal_chk(varr, dtype=float)

FileNotFoundError Traceback (most recent call last)
Cell In[15], line 1
----> 1 varr = load_videos(dpath, **param_load_videos)
2 chk, _ = get_optimal_chk(varr, dtype=float)

File C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\minian\utilities.py:104, in load_videos(vpath, pattern, dtype, downsample, downsample_strategy, post_process)
100 vlist = natsorted(
101 [vpath + os.sep + v for v in os.listdir(vpath) if re.search(pattern, v)]
102 )
103 if not vlist:
--> 104 raise FileNotFoundError(
105 "No data with pattern {}"
106 " found in the specified folder {}".format(pattern, vpath)
107 )
108 print("loading {} videos in folder {}".format(len(vlist), vpath))
110 file_extension = os.path.splitext(vlist[0])[1]

FileNotFoundError: No data with pattern video conversion[0].tiff found in the specified folder C:\WINDOWS\system32\inscopix_video

[leodiej]

Maybe the video is too heavy? What is the maximum input video size that minian can support?

[wmau]

You did not correctly define the file name pattern. Try param_load_videos = { "pattern": "video conversion .tiff", "dtype": np.uint8, "downsample": dict(frame=1, height=1, width=1), "downsample_strategy": "subset", }

…

On Wed, May 3, 2023, 9:31 AM leodiej ***@***.***> wrote: Maybe the video is too heavy? What is the mawimum input video size that minian can support? — Reply to this email directly, view it on GitHub <#241 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC4YH53UDUAX4KVE3MAUX3TXEJM3XANCNFSM6AAAAAAXUIDQ2E> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[leodiej]

I changed it and I got an error too. If I limit the number of slices and put in line 5 :
subset = dict(frame=slice(0, 499)) for example, would it work? I am thinking maybe the video is too heavy. It's a 35GB video.

[wmau]

Please always paste the full error in your message. It is difficult to diagnose without the error message.

…

On Wed, May 3, 2023, 9:48 AM leodiej ***@***.***> wrote: I changed it and I got an error too. If I limit the number of slices and put in line 5 : subset = dict(frame=slice(0, 499)) for example, would it work? I am thinking maybe the video is too heavy. It's a 35GB video. — Reply to this email directly, view it on GitHub <#241 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC4YH555CIESLLV5BRVGW5DXEJO3RANCNFSM6AAAAAAXUIDQ2E> . You are receiving this because you commented.Message ID: ***@***.***>

[leodiej]

ValueError Traceback (most recent call last)
Cell In[7], line 1
----> 1 varr = load_videos(dpath, **param_load_videos)
2 chk, _ = get_optimal_chk(varr, dtype=float)

File C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\minian\utilities.py:116, in load_videos(vpath, pattern, dtype, downsample, downsample_strategy, post_process)
114 movie_load_func = load_tif_lazy
115 else:
--> 116 raise ValueError("Extension not supported.")
118 varr_list = [movie_load_func(v) for v in vlist]
119 varr = darr.concatenate(varr_list, axis=0)

ValueError: Extension not supported.

[wmau]

Try renaming your file extension to .tif instead of .tiff. Make sure to also change param_load_videos

…

On Wed, May 3, 2023, 10:06 AM leodiej ***@***.***> wrote: ValueError Traceback (most recent call last) Cell In[7], line 1 ----> 1 varr = load_videos(dpath, **param_load_videos) 2 chk, _ = get_optimal_chk(varr, dtype=float) File C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\minian\utilities.py:116, in load_videos(vpath, pattern, dtype, downsample, downsample_strategy, post_process) 114 movie_load_func = load_tif_lazy 115 else: --> 116 raise ValueError("Extension not supported.") 118 varr_list = [movie_load_func(v) for v in vlist] 119 varr = darr.concatenate(varr_list, axis=0) ValueError: Extension not supported. — Reply to this email directly, view it on GitHub <#241 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC4YH57ID65AVBJYE66UVR3XEJQ5LANCNFSM6AAAAAAXUIDQ2E> . You are receiving this because you commented.Message ID: ***@***.***>

[wmau]

It is also possible minian cannot support the BigTiff format so you may need a preprocessing step to divide up the file into smaller tifs.

…

On Wed, May 3, 2023, 10:22 AM William Mau ***@***.***> wrote: Try renaming your file extension to .tif instead of .tiff. Make sure to also change param_load_videos On Wed, May 3, 2023, 10:06 AM leodiej ***@***.***> wrote: > ValueError Traceback (most recent call last) > Cell In[7], line 1 > ----> 1 varr = load_videos(dpath, **param_load_videos) > 2 chk, _ = get_optimal_chk(varr, dtype=float) > > File > C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\minian\utilities.py:116, > in load_videos(vpath, pattern, dtype, downsample, downsample_strategy, > post_process) > 114 movie_load_func = load_tif_lazy > 115 else: > --> 116 raise ValueError("Extension not supported.") > 118 varr_list = [movie_load_func(v) for v in vlist] > 119 varr = darr.concatenate(varr_list, axis=0) > > ValueError: Extension not supported. > > — > Reply to this email directly, view it on GitHub > <#241 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AC4YH57ID65AVBJYE66UVR3XEJQ5LANCNFSM6AAAAAAXUIDQ2E> > . > You are receiving this because you commented.Message ID: > ***@***.***> >

[leodiej]

I renamed the file extension to .tif and apriori it works. Thank you for your help.

[leodiej]

Hi.
I have get a problem with the video displaying. Then I tried to load an other one and still, "The extension is not suppported".

Set up Initial Basic Parameters#

minian_path = "."
dpath = "./inscopix/"
minian_ds_path = os.path.join(dpath, "minian2")
intpath = "./minian_intpath"
subset = dict(frame=slice(0, None))
subset_mc = None
interactive = True
output_size = 100
n_workers = int(os.getenv("MINIAN_NWORKERS", 4))
param_save_minian = {
"dpath": minian_ds_path,
"meta_dict": dict(session=-1, animal=-2),
"overwrite": True,
}

Pre-processing Parameters#

param_load_videos = {
"pattern": "2021-08-10-13-39-53_video_trig_0.tif",
"dtype": np.uint8,
"downsample": dict(frame=1, height=1, width=1),
"downsample_strategy": "subset",
}
param_denoise = {"method": "median", "ksize": 7}
param_background_removal = {"method": "tophat", "wnd": 15}

Motion Correction Parameters#

subset_mc = None
param_estimate_motion = {"dim": "frame"}

Initialization Parameters#

param_seeds_init = {
"wnd_size": 1000,
"method": "rolling",
"stp_size": 500,
"max_wnd": 15,
"diff_thres": 3,
}
param_pnr_refine = {"noise_freq": 0.06, "thres": 1}
param_ks_refine = {"sig": 0.05}
param_seeds_merge = {"thres_dist": 10, "thres_corr": 0.8, "noise_freq": 0.06}
param_initialize = {"thres_corr": 0.8, "wnd": 10, "noise_freq": 0.06}
param_init_merge = {"thres_corr": 0.8}

CNMF Parameters#

param_get_noise = {"noise_range": (0.06, 0.5)}
param_first_spatial = {
"dl_wnd": 10,
"sparse_penal": 0.01,
"size_thres": (25, None),
}
param_first_temporal = {
"noise_freq": 0.06,
"sparse_penal": 1,
"p": 1,
"add_lag": 20,
"jac_thres": 0.2,
}
param_first_merge = {"thres_corr": 0.8}
param_second_spatial = {
"dl_wnd": 10,
"sparse_penal": 0.01,
"size_thres": (25, None),
}
param_second_temporal = {
"noise_freq": 0.06,
"sparse_penal": 1,
"p": 1,
"add_lag": 20,
"jac_thres": 0.4,
}

os.environ["OMP_NUM_THREADS"] = "1"
os.environ["MKL_NUM_THREADS"] = "1"
os.environ["OPENBLAS_NUM_THREADS"] = "1"
os.environ["MINIAN_INTPATH"] = intpath

varr = load_videos(dpath, **param_load_videos)
chk, _ = get_optimal_chk(varr, dtype=float)

KeyError Traceback (most recent call last)
File C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\tifffile\tifffile.py:3142, in TiffFile.init(self, arg, mode, name, offset, size, _multifile, _useframes, _parent, **kwargs)
3141 try:
-> 3142 byteorder = {b'II': '<', b'MM': '>', b'EP': '<'}[header[:2]]
3143 except KeyError:

KeyError: b'\xa0\x00'

During handling of the above exception, another exception occurred:

TiffFileError Traceback (most recent call last)
Cell In[7], line 1
----> 1 varr = load_videos(dpath, **param_load_videos)
2 chk, _ = get_optimal_chk(varr, dtype=float)

File C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\minian\utilities.py:118, in load_videos(vpath, pattern, dtype, downsample, downsample_strategy, post_process)
115 else:
116 raise ValueError("Extension not supported.")
--> 118 varr_list = [movie_load_func(v) for v in vlist]
119 varr = darr.concatenate(varr_list, axis=0)
120 varr = xr.DataArray(
121 varr,
122 dims=["frame", "height", "width"],
(...)
127 ),
128 )

File C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\minian\utilities.py:118, in (.0)
115 else:
116 raise ValueError("Extension not supported.")
--> 118 varr_list = [movie_load_func(v) for v in vlist]
119 varr = darr.concatenate(varr_list, axis=0)
120 varr = xr.DataArray(
121 varr,
122 dims=["frame", "height", "width"],
(...)
127 ),
128 )

File C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\minian\utilities.py:161, in load_tif_lazy(fname)
147 def load_tif_lazy(fname: str) -> darr.array:
148 """
149 Lazy load a tif stack of images.
150
(...)
159 Resulting dask array representation of the tif stack.
160 """
--> 161 data = TiffFile(fname)
162 f = len(data.pages)
164 fmread = da.delayed(load_tif_perframe)

File C:\ProgramData\Anaconda3\envs\minian2\lib\site-packages\tifffile\tifffile.py:3144, in TiffFile.init(self, arg, mode, name, offset, size, _multifile, _useframes, _parent, **kwargs)
3142 byteorder = {b'II': '<', b'MM': '>', b'EP': '<'}[header[:2]]
3143 except KeyError:
-> 3144 raise TiffFileError(f'not a TIFF file {header!r}')
3146 version = struct.unpack(byteorder + 'H', header[2:4])[0]
3147 if version == 43:
3148 # BigTiff

TiffFileError: not a TIFF file b'\xa0\x00\xa0\n'