referenced frame series could not be found

[Pankaj Vilas Jadhav]

Hi all,

I am using warp2.0, i am getting the following error while trying to import titseires to get the .tomostar file:

Failed to parse TS_001.mrc.mdoc: At least one of the referenced frame series could not be found:

Any suggestions what must be going wrong?

Pankaj

[Pankaj Vilas Jadhav]

Thanks Alister,

Will try that.

Also, I wasn't sure if it was a bug or just something I was doing wrong.

Thanks again!

Pankaj.

On Thu, Jun 13, 2024 at 12:18 PM Alister Burt <alist...@gmail.com> wrote:

Thanks Pankaj, 

I've investigated a bit and found the likely source of the bug but haven't fixed yet - you can see that outlined here https://github.com/warpem/warp/issues/143

In future if you come across bugs could you pop up in the github issues rather than the mailing list? It's easier to keep track of things

If you need a temporary solution since it looks like a problem with path parsing I would try renaming both files and subframe path entries in the mdocs to something else

Cheers,

Alister

On Thu, 13 Jun 2024 at 06:01, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:

Hi Alister,

I didn't realize that the mail just went to you.

Here are the commands I used;

##Create Frame Series Settings File:

WarpTools create_settings --folder_data frames --folder_processing warp_frameseries --output warp_frameseries.settings --extension "*.tif" --angpix 1.667 --gain_path CountRef_2024-04-14_17.44.31_TS_001_12.0.mrc --gain_flip_y --exposure 3.31076

##Create Tilt Series Settings File:

WarpTools create_settings --folder_data tomostar --folder_processing warp_tiltseries --output warp_tiltseries.settings --extension "*.tomostar" --angpix 1.667 --gain_path CountRef_2024-04-14_17.44.31_TS_001_12.0.mrc --gain_flip_y --exposure 3.31076 --tomo_dimensions 4092x5760x1500

##Frame Series Motion and CTF Estimation:

WarpTools fs_motion_and_ctf --settings warp_frameseries.settings --m_grid 1x1x3 --c_grid 2x2x1 --c_range_max 7 --c_defocus_max 8 --c_use_sum --out_averages --out_average_halves

##Import Tilt Series Metadata:

WarpTools ts_import --mdocs mdoc --frameseries warp_frameseries --tilt_exposure 3.31076 --min_intensity 0.2 --dont_invert --output tomostar

PFA screenshots of the directories content.

Thanks,

Pankaj

On Thu, Jun 13, 2024 at 1:43 AM Alister Burt <alist...@gmail.com> wrote:

Hi Pankaj,

Could you try to reply all in mailing list conversations? It helps keep everyone in the loop :-)

Can you please paste

- the command you used to create your frame series settings file

- the command you used to create your tilt series settings file

- the command you used for ts_import

and whether frame series processing worked fine?

Thanks!

Alister

On Tue, 11 Jun 2024 at 16:20, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:

Hi Alister,

Thanks for your response.

Yes, the filenames in the mdoc and the frames data folder are the same.

Thanks,

Pankaj

On Tue, Jun 11, 2024 at 6:32 PM Alister Burt <alist...@gmail.com> wrote:

Hi Pankaj,

Do the file names in your mdoc files match the file names in your frame series data folder?

Alister

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[Pankaj Vilas Jadhav]

Hi Alister,

I have shared the entire content of the mdoc file in the github issue.

Thanks, 

Pankaj.

On Thu, Jun 13, 2024 at 5:52 PM Alister Burt <alist...@gmail.com> wrote:

Hi Pankaj, 

I've taken a closer look and the filename from the section of the mdoc you sent parses correctly - could you please paste the whole contents of your mdoc in the github issue and double check that there is nothing weird in your mdoc?

Cheers,

Alister

On Thu, 13 Jun 2024 at 12:22, Alister Burt <alist...@gmail.com> wrote:

Yes I think it’s likely a bug - everything you did looks reasonable at first glance!

Sent from mobile - apologies for brevity

On Jun 13, 2024, at 11:57, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:



<Screenshot 2024-06-13 at 8.58.57 AM.png>

<Screenshot 2024-06-13 at 8.43.42 AM.png>

<Screenshot 2024-06-13 at 8.41.22 AM.png>

<Screenshot 2024-06-11 at 5.22.16 PM.png>

[Alister Burt]

Hi Pankaj,

Could you try to reply all in mailing list conversations? It helps keep everyone in the loop :-)

Can you please paste

- the command you used to create your frame series settings file

- the command you used to create your tilt series settings file

- the command you used for ts_import

and whether frame series processing worked fine?

Thanks!

Alister

On Tue, 11 Jun 2024 at 16:20, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:

Hi Alister,

Thanks for your response.

Yes, the filenames in the mdoc and the frames data folder are the same.

Thanks,

Pankaj

On Tue, Jun 11, 2024 at 6:32 PM Alister Burt <alist...@gmail.com> wrote:

Hi Pankaj,

Do the file names in your mdoc files match the file names in your frame series data folder?

Alister

On Tue, 11 Jun 2024 at 16:07, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:

--

[Alister Burt]

Hi Pankaj,

Do the file names in your mdoc files match the file names in your frame series data folder?

Alister

On Tue, 11 Jun 2024 at 16:07, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:

--

[Alister Burt]

Hi Pankaj, 

I've taken a closer look and the filename from the section of the mdoc you sent parses correctly - could you please paste the whole contents of your mdoc in the github issue and double check that there is nothing weird in your mdoc?

Cheers,

Alister

On Thu, 13 Jun 2024 at 12:22, Alister Burt <alist...@gmail.com> wrote:

Yes I think it’s likely a bug - everything you did looks reasonable at first glance!

Sent from mobile - apologies for brevity

On Jun 13, 2024, at 11:57, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:



<Screenshot 2024-06-13 at 8.58.57 AM.png>

<Screenshot 2024-06-13 at 8.43.42 AM.png>

<Screenshot 2024-06-13 at 8.41.22 AM.png>

<Screenshot 2024-06-11 at 5.22.16 PM.png>

[Alister Burt]

Yes I think it’s likely a bug - everything you did looks reasonable at first glance!

Sent from mobile - apologies for brevity

On Jun 13, 2024, at 11:57, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:



<Screenshot 2024-06-13 at 8.58.57 AM.png>

<Screenshot 2024-06-13 at 8.43.42 AM.png>

<Screenshot 2024-06-13 at 8.41.22 AM.png>

<Screenshot 2024-06-11 at 5.22.16 PM.png>

[Alister Burt]

Thanks Pankaj, 

I've investigated a bit and found the likely source of the bug but haven't fixed yet - you can see that outlined here https://github.com/warpem/warp/issues/143

In future if you come across bugs could you pop up in the github issues rather than the mailing list? It's easier to keep track of things

If you need a temporary solution since it looks like a problem with path parsing I would try renaming both files and subframe path entries in the mdocs to something else

Cheers,

Alister

On Thu, 13 Jun 2024 at 06:01, Pankaj Vilas Jadhav <pvja...@umich.edu> wrote:

Hi Alister,

I didn't realize that the mail just went to you.

Here are the commands I used;

##Create Frame Series Settings File:

WarpTools create_settings --folder_data frames --folder_processing warp_frameseries --output warp_frameseries.settings --extension "*.tif" --angpix 1.667 --gain_path CountRef_2024-04-14_17.44.31_TS_001_12.0.mrc --gain_flip_y --exposure 3.31076

##Create Tilt Series Settings File:

WarpTools create_settings --folder_data tomostar --folder_processing warp_tiltseries --output warp_tiltseries.settings --extension "*.tomostar" --angpix 1.667 --gain_path CountRef_2024-04-14_17.44.31_TS_001_12.0.mrc --gain_flip_y --exposure 3.31076 --tomo_dimensions 4092x5760x1500

##Frame Series Motion and CTF Estimation:

WarpTools fs_motion_and_ctf --settings warp_frameseries.settings --m_grid 1x1x3 --c_grid 2x2x1 --c_range_max 7 --c_defocus_max 8 --c_use_sum --out_averages --out_average_halves

##Import Tilt Series Metadata:

WarpTools ts_import --mdocs mdoc --frameseries warp_frameseries --tilt_exposure 3.31076 --min_intensity 0.2 --dont_invert --output tomostar

PFA screenshots of the directories content.

Thanks,

Pankaj

[Pankaj Vilas Jadhav]

Hi Alister,

I didn't realize that the mail just went to you.

Here are the commands I used;

##Create Frame Series Settings File:

WarpTools create_settings --folder_data frames --folder_processing warp_frameseries --output warp_frameseries.settings --extension "*.tif" --angpix 1.667 --gain_path CountRef_2024-04-14_17.44.31_TS_001_12.0.mrc --gain_flip_y --exposure 3.31076

##Create Tilt Series Settings File:

WarpTools create_settings --folder_data tomostar --folder_processing warp_tiltseries --output warp_tiltseries.settings --extension "*.tomostar" --angpix 1.667 --gain_path CountRef_2024-04-14_17.44.31_TS_001_12.0.mrc --gain_flip_y --exposure 3.31076 --tomo_dimensions 4092x5760x1500

##Frame Series Motion and CTF Estimation:

WarpTools fs_motion_and_ctf --settings warp_frameseries.settings --m_grid 1x1x3 --c_grid 2x2x1 --c_range_max 7 --c_defocus_max 8 --c_use_sum --out_averages --out_average_halves

##Import Tilt Series Metadata:

WarpTools ts_import --mdocs mdoc --frameseries warp_frameseries --tilt_exposure 3.31076 --min_intensity 0.2 --dont_invert --output tomostar

PFA screenshots of the directories content.

Thanks,

Pankaj