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).::
Replace ``curve`` with ``playlist`` in the above commands to navigate
around through the list of loaded playlists.
+Because the playlist name is usually saved in the playlist file
+itself, there is a ``name_playlist`` command that allows you to rename
+playlists on the fly.
+
+ hooke> name_playlist 'my old playlist'
+
Taking notes
------------
If you don't want the entire block, try the ``cut`` command.
-Interacting with the plot
--------------------------
+Analysis
+--------
-(no plots in command line mode...)
+The commands we have covered so far allow basic bookkeeping. The
+point of Hooke, though, is to allow you to easily analyze force
+spectroscopy data. We cover those analysis commands in this section.
Measuring distances and forces
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Worm like chain and freely jointed chain fitting
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.. todo:: Update WLC fitting tutorial section.
-
-You can measure by hand the parameters relative to a force peak using
-a worm-like chain fitting with the ``fit`` command. The command by
-default automatically finds the contact point, asks for two points
-delimiting the portion to fit, and performs a two-variable fit, with
-contour length, persistence length, and their relative errors as
-output. If desired, one can use the ``noauto`` option to manually
-click the contact point, and/or the ``pl=NUMBER`` options to impose a
-specific persistence or Kuhn length (in nanometers). You can choose
-which model to use with ``set fit_function wlc`` or ``set fit_function
-fjc``. See the help of the ``fit`` command from the Hooke command
-line for details.
-
-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.
-
-Fast curve reviewing and saving
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. todo:: Update curve review tutorial section.
-
-When automatic routines are not good enough to filter your data, use
-``review`` command to cycle through your playlist presenting ten
-curves in the same graph. You can then enter the numbers of the
-interesting curves and automatically save a copy of them into another
-directory.
+Polymer model fitting is a complicated beast. To correctly fit your
+chosen model (WLC, FJC, etc.), you need to execute a multi-step
+analysis. Hooke provides a flexible chain of curve analyisis commands
+that create new data columns (e.g. `deflection (N)`) or store
+information in a curve's `info` dictionary (e.g. `flat filter peaks`).
+You can, if necessary, adjust the names of input and output columns
+and `info` values to combine the available commands in new and useful
+ways.::
+
+ 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> 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
+
+.. _PyYAML: http://pyyaml.org/
+
+Command stacks
+~~~~~~~~~~~~~~
+
+Since you are likely to apply similar analysis to several curves,
+Hooke provides :mod:`command stacks <hooke.command_stack>` for
+bundling groups of commands.::
+
+ hooke> start_command_capture
+ hooke> zero_surface_contact_point --block retract
+ hooke> flat_filter_peaks --block retract --min_points 1
+ ...
+ hooke> stop_command_capture
+
+You can check the state of the command stack with
+``get_command_stack`` and the state of capture with
+``get_command_capture_state``. If you make mistakes, you can pop
+commands from the stack with ``pop_command_from_stack``. If you stop
+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).::
+
+ hooke> save_command_stack --output my_stack
+ hooke> load_command_stack --input my_stack
+
+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> block_info --block retract --output data.yaml name 'polymer peak [0-9]*'
+ hooke> stop_command_capture
+ hooke> apply_command_stack_to_playlist
Configuring Hooke
-----------------
projects / hooke.git / blobdiff