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--- pipeline:movie:sxunblur [2018/02/27 13:58]
moriya
+++ pipeline:movie:sxunblur [2018/02/27 18:04]
moriya
@@ Line 55: / Line 55: @@
 === Advanced Parameters ===
   ; %%--%%save_frames : Save aligned movie frames: Save aligned movie frames. This option slows down the process. (default False)
-  ; %%--%%skip_dose_filter : Apply dose filter: Indicate if dose filter should be applied or not. With this option, voltage, exposure per frame, and pre exposure will be ignored. By default, apply dose filter. (default False question reversed in GUI)
+  ; %%--%%skip_dose_filter : Apply dose filter: Indicate if dose filter should be applied or not. With this option, %%--%%voltage, %%--%%exposure_per_frame, and %%--%%pre_exposure will be ignored. By default, apply dose filter. (default False question reversed in GUI)
   ; %%--%%expert_mode : Use expert mode: Requires %%--%%initial_shift, %%--%%shift_radius, %%--%%b_factor, %%--%%fourier_vertical, %%--%%fourier_horizontal, %%--%%shift_threshold, %%--%%iterations, %%--%%dont_restore_noise, and %%--%%verbosity options. (default False)
   ; %%--%%shift_initial : Minimum shift for initial search [A]: Effective only when %%--%%expert_mode option is used. (default 2.0)
@@ Line 71: / Line 71: @@
 The program automatically creates the following subdirectories in the specified output directory.
-__Run without dose-filtering__:
+\\ __Run without dose-filtering__:
-  * Sum files will be written to the "corrsum" directory.
+  * Sum files will be written to the ''corrsum'' directory.
-  * Log files will be written to the "logfiles" directory.
+  * Log files will be written to the ''logfiles'' directory.
-  * Aligned frames will be written to the "corrsum" directory.
+  * Aligned frames will be written to the ''corrsum'' directory.
-  * Shift files  will be written to the "shift" directory.
+  * Shift files  will be written to the ''shift'' directory.
-  * FRC files will be written to the "frc" directory.
+  * FRC files will be written to the ''frc'' directory.
-__Run with dose-filtering (as without dose-filtering plus)__:
+\\ __Run with dose-filtering (as without dose-filtering plus)__:
-  * Dose filtered sum files will be written to the "corrsum_dose_filtered" directory.
+  * Dose filtered sum files will be written to the ''corrsum_dose_filtered'' directory.
-  * Log files will be written to the "logfiles" directory.
+  * Log files will be written to the ''logfiles'' directory.
-  * Dose filtered aligned frames will be written to the "corrsum_dose_filtered" directory.
+  * Dose filtered aligned frames will be written to the ''corrsum_dose_filtered'' directory.
-  * Shift files  will be written to the "shift" directory.
+  * Shift files  will be written to the ''shift'' directory.
-  * FRC files will be written to the "frc" directory.
+  * FRC files will be written to the ''frc'' directory.
 \\

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