test/data/vclamp_jpk/README: Document sample versions

[hooke.git] / doc / tutorial.txt

diff --git a/doc/tutorial.txt b/doc/tutorial.txt
index 65d288ec7e74eb801cd14d04aed0900b70149889..1e0b95709410e6d451b50dc9d2eed84e1e5fd602 100644 (file)
--- a/doc/tutorial.txt
+++ b/doc/tutorial.txt
@@ -106,13 +106,20 @@ and you want to analyze them all.
 
 You then can ``cd`` (change directory) to the directory::
 
-    hooke> cd --path c:\curves
+    hooke> cd --path "c:\curves"
 
-Type ``pwd`` (print working directory) to check the directory is correct.::
+Hooke parses it's commandline using `POSIX rules`_, so you need to
+quote arguments with backslashes to keep them from being expanded as
+escape sequences (e.g. ``\t`` → ``TAB``).
+
+Type ``pwd`` (print working directory) to check the directory is
+correct.::
 
     hooke> pwd
     c:\curves
 
+.. _POSIX rules: http://docs.python.org/library/shlex#parsing-rules
+
 You can list the files in the directory using ``ls`` or ``dir``
 (they’re synonyms).::
 
@@ -308,9 +315,24 @@ ways.::
     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> block_info --block retract --output data.yaml name 'polymer peak [0-9]*'
+
+This stores the fit parameters in the block's
+:attr:`~hooke.curve.Data.info` dictionary and also appends them to
+:file:`data.yaml` (see each command's `Help`_ for details).  To access
+the parameters, load :file:`data.yaml` with PyYAML_::
+
+    $ python
+    >>> import yaml
+    >>> import hooke.util.yaml
+    >>> data = yaml.load(open('data.yaml', 'r'))
+
+and extract your parameter::
+
+    >>> data['20071120a_i27_t33.100']['retract']['polymer peak 0']['contour length (m)']
+    2.124...e-08
 
-See each command's `Help`_ for details.
+.. _PyYAML: http://pyyaml.org/
 
 Command stacks
 ~~~~~~~~~~~~~~
@@ -368,7 +390,7 @@ freely jointed chain fitting`_ and `Command stacks`_.::
     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> block_info --block retract --output data.yaml name 'polymer peak [0-9]*'
     hooke> stop_command_capture
     hooke> apply_command_stack_to_playlist