Re: [scipion-users] DM4 to MRC conversion flips gain reference?

[Pablo C. <pc...@cn...>]

<div dir='auto'>hi Matt, since motioncor does not accept dm4, scipion is using xmipp to convert dm4 to mrc and there, the flip on Y is happening.&nbsp;<div dir="auto"><br></div><div dir="auto">We will try to investigate more, but meanwhile:</div><div dir="auto"><br></div><div dir="auto">Gain in dm4 will require flip on Y in motioncor 2, and I guess the rest of the alignment protocols.</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 28 ago. 2019 1:16, Matt Harrington &lt;ma...@ms...&gt; escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Our users report that the motioncor2 protocol flips the gain reference&#13;<br>
when converting from .dm4 to .mrc.&nbsp; I see an option in the MC2&#13;<br>
protocol to flip the gain reference back.&nbsp; However, I'm wondering why&#13;<br>
the gain reference is flipped in the first place.&#13;<br>
&#13;<br>
This code seems relevant:&#13;<br>
&#13;<br>
https://github.com/I2PC/scipion/blob/d1a60f69960d1079bbbecde5bf3f5f4017b36927/pyworkflow/em/convert/image_handler.py#L178&#13;<br>
&#13;<br>
However, since *.img files are not involved I would guess the "else"&#13;<br>
branch of that statement would be followed, meaning that Xmipp&#13;<br>
performs the conversion.&#13;<br>
&#13;<br>
Any ideas how to troubleshoot this?&#13;<br>
&#13;<br>
Matt&#13;<br>
&#13;<br>
&#13;<br>
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</blockquote></div><br></div>