Flesh out command stack execution.

[hooke.git] / doc / tutorial.txt

diff --git a/doc/tutorial.txt b/doc/tutorial.txt
index 4ae616b83dd5999a0d6cc5e04fb5393d2249af4b..a2ff0cc336a112ac3931c98b1653b1364aa73be1 100644 (file)
--- a/doc/tutorial.txt
+++ b/doc/tutorial.txt
@@ -327,23 +327,44 @@ capturing a command stack (e.g. to test a complicated command before
 continuing), you can continue adding to the same stack with
 ``restart_command_capture.``
 
+To execute a command stack, run::
+
+    hooke> execute_command_stack
+
+To execute a command stack on every curve in a playlist, run::
+
+    hooke> apply_command_stack_to_playlist
+
+If you decide that there are commands in a curve's stack that you
+don't want, you can clear the stack with::
+
+    hooke> clear_curve_command_stack
+
 You can also save command stacks to disk (and reload them later,
-potentially in a different Hooke session).
+potentially in a different Hooke session).::
 
     hooke> save_command_stack --output my_stack
     hooke> load_command_stack --input my_stack
 
-Multiple curve fitting and measuring
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.. todo:: Update multiple curve fitting tutorial section.
-
-You can cycle through all your current playlist obtaining WLC fit, FJC
-fit, rupture force and slope (loading rate) information from each
-curve using the ``multifit`` command.  The collected data can be saved
-in a text file for further analysis in your favourite spreadsheet or
-statistical program.  If you want to check your parameters on the
-current curve before fitting all the files in your playlist, use
-``multifit justone``.  See the ``multifit`` help for more options.
+Multiple curve analysis
+~~~~~~~~~~~~~~~~~~~~~~~
+
+You can analyze multiple curves by combining `Worm like chain and
+freely jointed chain fitting`_ and `Command stacks`_.::
+
+    hooke> start_command_capture
+    hooke> zero_surface_contact_point --block retract
+    hooke> flat_filter_peaks --block retract --min_points 1
+    hooke> zero_surface_contact_point --block retract
+    ...        --ignore_after_last_peak_info_name 'flat filter peaks'
+    hooke> convert_distance_to_force --block retract
+    ...        --deflection_column 'surface deflection (m)'
+    hooke> remove_cantilever_from_extension --block retract
+    hooke> flat_peaks_to_polymer_peaks --block retract
+    hooke> polymer_fit_peaks --block retract
+    hooke> export_block --block retract --output myblock.dat
+    hooke> stop_command_capture
+    hooke> apply_command_stack_to_playlist
 
 Fast curve reviewing and saving
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~