Don't specify curve or data block types. See doc/standards.txt.

diff --git a/doc/analysis.txt b/doc/analysis.txt
new file mode 100644 (file)
index 0000000..1286393
--- /dev/null
+++ b/doc/analysis.txt
@@ -0,0 +1,85 @@
+******************
+Analysis templates
+******************
+
+.. toctree::
+   :maxdepth: 2
+
+Overview
+========
+
+Hooke is a large, flexible beast, and the number of available commands
+can be intimidating.  In this section, we'll lay out the procedure for
+analyzing a number of common experiment types.  The experiment types
+are arranged in the order that they were developed, citating the first
+known paper in each class.  If we've got a citation wrong, please
+submit a bug report (:doc:`bugs`).
+
+
+Velocity clamp force spectroscopy
+=================================
+
+Developed by Rief et al. [#rief1997]_, velocity clamp spectroscopy
+measures domain unfolding forces as the tip is moved away from the
+surface at a constant velocity.
+
+.. todo:: Velocity clamp example plot.
+
+Basic analysis is something like::
+
+    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]*'
+
+The unfolding forces should be grouped by pull velocity, and the resulting
+distributions can be fit to specific unfolding models by comparison with
+monte-carlo simulations (see, for example, sawsim_).
+
+.. [#rief1997] M. Rief, M. Gautel, F. Oesterhelt, J.M. Fernandez,
+  H.E. Gaub.
+  "Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM."
+  Science, 1997.
+  doi: `10.1126/science.276.5315.1109 <http://dx.doi.org/10.1126/science.276.5315.1109>`_
+
+.. _sawsim: http://www.physics.drexel.edu/~wking/sawsim/
+
+Force clamp spectroscopy
+========================
+
+Developed by Fernandez and Li [#fernandez2004]_, force clamp spectroscopy
+measures the lifetime of a domain's folded state while subject to a constant
+tension.
+
+.. todo:: Force clamp example plot.
+
+.. todo:: Force clamp example analysis.
+
+.. [#fernandez2004] J.M. Fernandez, H. Li.
+  "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a
+  Single Protein."
+  Science, 2004.
+  doi: `10.1126/science.1092497 <http://dx.doi.org/10.1126/science.1092497>`_
+
+Two-color fluorescence coincidence spectroscopy
+===============================================
+
+Developed by Clarke et al. [#clarke2007]_,...
+
+.. todo:: TCCS explanation.
+
+.. todo:: TCCS example plot.
+
+.. todo:: TCCS example analysis.
+
+.. [#clarke2007] R.W. Clarke, A. Orte, D. Klenerman.
+  "Optimized Threshold Selection for Single-Molecule Two-Color
+  Fluorescence Coincidence Spectroscopy."
+  Anal. Chem., 2007.
+  doi: `10.1021/ac062188w <http://dx.doi.org/10.1021/ac062188w>`_

diff --git a/doc/index.txt b/doc/index.txt
index 37a1167b81e7e32a3ed7d304ddb3c8b4e479db3b..a067fb7f6731b1b4ae324ff0a1ec4e8a9ec1b754 100644 (file)
--- a/doc/index.txt
+++ b/doc/index.txt
@@ -28,9 +28,11 @@ Contents
 
    install
    tutorial
 
    install
    tutorial

+   analysis

    config
    bugs
    hacking
    config
    bugs
    hacking

+   standards

    hooke/hooke
    doc
 
    hooke/hooke
    doc
 

diff --git a/doc/standards.txt b/doc/standards.txt
new file mode 100644 (file)
index 0000000..743b9aa
--- /dev/null
+++ b/doc/standards.txt
@@ -0,0 +1,63 @@
+********************
+Standard experiments
+********************
+
+.. toctree::
+   :maxdepth: 2
+
+Overview
+========
+
+Force spectroscopy experiments are generally classified as "force
+clamp", "velocity clamp", etc..  While previous versions of Hooke
+attempted to reproduce such classification, I now believe this
+classification is counter-productive.  The type of experiment carried
+out by a given :class:`~hooke.curve.Curve` is determined by the
+sequence of :class:`~hooke.curve.Data` blocks in the curve.  For
+example, a classic velocity clamp experiment would look like::
+
+    hooke> curve_info --enable-block_names
+    block names: ['approach', 'pause', 'retract']
+
+And classic force clamp experiment would look like::
+
+    hooke> curve_info --enable-block_names
+    block names: ['approach', 'pause', 'retract', 'force clamp']
+
+However, the situation is complicated by refolding experiments such as::
+
+    hooke> curve_info --enable-block_names
+    block names: ['approach-0', 'pause-0', 'retract-0',
+                  'approach-1', 'pause-1', 'retract-1',
+                  'approach-2', 'pause-2', 'retract-2',
+                 ...]
+
+The benefit to classifying curves in Hooke is that each class of
+experiment has a standard analysis procedure (e.g. unfolding force
+extraction for velocity clamp experiments or survival time extraction
+for force clamp experiments).  However, the potential convenience of
+Hooke being able to guess a user's desired analysis is outweighed by
+the increased complexity and rigidity that such guessing requires.
+Instead we provide :class:`~hooke.command.Command`\s that can be
+applied to any data block, and leave it up to the user to construct a
+sequence of analysis commands that makes sense.  The risk to this
+flexible approach is confusion for both the user and the Hooke
+developer.  The remainder of this section lays out a scheme for
+maintaining developer sanity.  Users should read over the
+:doc:`analysis` section for an overview of analysis procedures
+that are standardized enough to have written documentation.
+
+Drivers
+=======
+
+.. todo:: Explain driver responsibilities.
+
+Commands
+========
+
+.. todo:: Explain command analysis and storage behaviour.
+
+Results
+=======
+
+.. todo:: Explain procedure for exporting analysis results.

diff --git a/hooke/curve.py b/hooke/curve.py
index fc8701b0b98a5f21b8d9fd0a1dd195be12251849..030efcbab3601b6a0608dc908d0bbe1b6b2b6dec 100644 (file)
--- a/hooke/curve.py
+++ b/hooke/curve.py
@@ -28,7 +28,6 @@ import os.path
 import numpy
 
 from .command_stack import CommandStack
 import numpy
 
 from .command_stack import CommandStack

-from . import experiment

 
 
 class NotRecognized (ValueError):
 
 
 class NotRecognized (ValueError):


@@ -156,23 +155,14 @@ class Curve (object):
     would consist of the approach data and the retract data.  Metadata
     would be the temperature, cantilever spring constant, etc.
 
     would consist of the approach data and the retract data.  Metadata
     would be the temperature, cantilever spring constant, etc.
 

-    Two important :attr:`info` settings are `filetype` and
-    `experiment`.  These are two strings that can be used by Hooke
-    commands/plugins to understand what they are looking at.
-
-    * :attr:`info['filetype']` should contain the name of the exact
-      filetype defined by the driver (so that filetype-speciofic
-      commands can know if they're dealing with the correct filetype).
-    * :attr:`info['experiment']` should contain an instance of a
-      :class:`hooke.experiment.Experiment` subclass to identify the
-      experiment type.  For example, various
-      :class:`hooke.driver.Driver`\s can read in force-clamp data, but
-      Hooke commands could like to know if they're looking at force
-      clamp data, regardless of their origin.
-
-    Another important attribute is :attr:`command_stack`, which holds
-    a :class:`~hooke.command_stack.CommandStack` listing the commands
-    that have been applied to the `Curve` since loading.
+    Each :class:`Data` block in :attr:`data` must contain an
+    :attr:`info['name']` setting with a unique (for the parent
+    curve) name identifying the data block.  This allows plugins 
+    and commands to access individual blocks.
+
+    Each curve maintiains a :class:`~hooke.command_stack.CommandStack`
+    (:attr:`command_stack`) listing the commands that have been
+    applied to the `Curve` since loading.

 
     The data-type is pickleable, to ensure we can move it between
     processes with :class:`multiprocessing.Queue`\s.
 
     The data-type is pickleable, to ensure we can move it between
     processes with :class:`multiprocessing.Queue`\s.

diff --git a/hooke/driver/__init__.py b/hooke/driver/__init__.py
index bc38a24515b78f08dd158a934095ada0927971b7..8704f5d58cfa072bf77938f1590144bc06d18307 100644 (file)
--- a/hooke/driver/__init__.py
+++ b/hooke/driver/__init__.py
@@ -89,9 +89,7 @@ class Driver (object):
         The input `info` :class:`dict` may contain attributes read
         from the :class:`~hooke.playlist.FilePlaylist`.
 
         The input `info` :class:`dict` may contain attributes read
         from the :class:`~hooke.playlist.FilePlaylist`.
 

-        The `info` :class:`dict` must contain values for the keys:
-        'filetype' and 'experiment'.  See :class:`hooke.curve.Curve`
-        for details.
+        See :class:`hooke.curve.Curve` for details.

         """
         raise NotImplementedError
 
         """
         raise NotImplementedError
 

diff --git a/hooke/driver/csvdriver.py b/hooke/driver/csvdriver.py
index 3ec4cbe054abe49178b273249a20a8c4e9d2a7e6..5713233c22863af8213f533a22ec59ba0aabf421 100644 (file)
--- a/hooke/driver/csvdriver.py
+++ b/hooke/driver/csvdriver.py
@@ -41,10 +41,6 @@ class csvdriverDriver(lib.driver.Driver):
         self.filedata = open(filename,'r')
         self.data = list(self.filedata)
         self.filedata.close()
         self.filedata = open(filename,'r')
         self.data = list(self.filedata)
         self.filedata.close()

-
-        self.filetype = 'generic'
-        self.experiment = ''
-

         self.filename=filename
 
     def close_all(self):
         self.filename=filename
 
     def close_all(self):

diff --git a/hooke/driver/hdf5.py b/hooke/driver/hdf5.py
index f338324fdb978a45f8f7d6021dab5ea54f2d83c8..64f09beed26431e6aac1b794098bd96249b9c404 100644 (file)
--- a/hooke/driver/hdf5.py
+++ b/hooke/driver/hdf5.py
@@ -35,9 +35,6 @@ class hdf5Driver(lhc.Driver):
         self.lines=list(self.filedata.readlines())
         self.filedata.close()
         
         self.lines=list(self.filedata.readlines())
         self.filedata.close()
         

-        self.filetype='hdf5'
-        self.experiment='smfs'
-        

     def close_all(self):
         self.filedata.close()
         
     def close_all(self):
         self.filedata.close()
         

diff --git a/hooke/driver/hemingway.py b/hooke/driver/hemingway.py
index af351f7d78f4eb2f0f26465d2513b278a41d4499..fe0fb98d92977be192e1aa016a073c9203b49b32 100644 (file)
--- a/hooke/driver/hemingway.py
+++ b/hooke/driver/hemingway.py
@@ -24,7 +24,6 @@ import os.path
 import numpy
 
 from .. import curve as curve
 import numpy
 
 from .. import curve as curve

-from .. import experiment as experiment

 from ..util.util import Closing as Closing
 from . import Driver as Driver
 
 from ..util.util import Closing as Closing
 from . import Driver as Driver
 


@@ -72,7 +71,5 @@ class HemingwayDriver (Driver):
         ret.info['name'] = 'force clamp'
         # assume 1 ms timestep
         ret[:,0] = numpy.arange(0, 1e-3*data.shape[0], 1e-3, dtype=ret.dtype)
         ret.info['name'] = 'force clamp'
         # assume 1 ms timestep
         ret[:,0] = numpy.arange(0, 1e-3*data.shape[0], 1e-3, dtype=ret.dtype)

-        
-        file_info['filetype'] = self.name
-        file_info['experiment'] = experiment.ForceClamp()
+

         return ([ret,], file_info)
         return ([ret,], file_info)

diff --git a/hooke/driver/jpk.py b/hooke/driver/jpk.py
index d70fa3cd7f7516c3784d51e848354f1aa531e191..8ca521d80ee3d78fe275cffdef09c25b3a1a6cb6 100644 (file)
--- a/hooke/driver/jpk.py
+++ b/hooke/driver/jpk.py
@@ -30,7 +30,6 @@ import zipfile
 import numpy
 
 from .. import curve as curve
 import numpy
 
 from .. import curve as curve

-from .. import experiment as experiment

 from ..util.util import Closing as Closing
 from ..util.si import join_data_label, split_data_label
 from . import Driver as Driver
 from ..util.util import Closing as Closing
 from ..util.si import join_data_label, split_data_label
 from . import Driver as Driver


@@ -148,16 +147,8 @@ class JPKDriver (Driver):
     def _zip_translate_params(self, params, chan_info):
         info = {
             'raw info':params,
     def _zip_translate_params(self, params, chan_info):
         info = {
             'raw info':params,

-            'filetype':self.name,

             #'time':self._time_from_TODO(raw_info[]),
             }
             #'time':self._time_from_TODO(raw_info[]),
             }

-        # TODO: distinguish between force clamp and velocity clamp
-        # experiments.  Note that the JPK file format is flexible
-        # enough to support mixed experiments (i.e. both force clamp
-        # and velocity clamp segments in a single experiment), but I
-        # have no idea what sort of analysis such experiments would
-        # require ;).
-        info['experiment'] = experiment.VelocityClamp()

         force_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['unit']['unit']
         assert force_unit == 'N', force_unit
         force_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['base-calibration-slot']
         force_unit = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['scaling']['unit']['unit']
         assert force_unit == 'N', force_unit
         force_base = chan_info['channel']['vDeflection']['conversion-set']['conversion']['force']['base-calibration-slot']

diff --git a/hooke/driver/mcs.py b/hooke/driver/mcs.py
index 50a50292819ab3b943e70143ad9ce87be74c79a4..5e80c51321756a8a46f7a553e70435cd26cb62f6 100644 (file)
--- a/hooke/driver/mcs.py
+++ b/hooke/driver/mcs.py
@@ -53,9 +53,6 @@ class mcsDriver(lib.driver.Driver):
         self.bluedata=self.filebluedata.read()
         self.filebluedata.close()
 
         self.bluedata=self.filebluedata.read()
         self.filebluedata.close()
 

-        self.filetype = 'mcs'
-        self.experiment = 'smfluo'
-

     def close_all(self):
         self.filedata.close()
         self.filebluedata.close()
     def close_all(self):
         self.filedata.close()
         self.filebluedata.close()

diff --git a/hooke/driver/mfp1d.py b/hooke/driver/mfp1d.py
index 2c314bdf0407f302ff22ff76e1784eb49319cc33..355ba44fcca6cec45d01d4e6e32419f995a7eea6 100644 (file)
--- a/hooke/driver/mfp1d.py
+++ b/hooke/driver/mfp1d.py
@@ -58,9 +58,6 @@ class mfp1dDriver(lib.driver.Driver):
         self.lines = list(self.filedata.readlines())
         self.filedata.close()
 
         self.lines = list(self.filedata.readlines())
         self.filedata.close()
 

-        self.filetype = 'mfp1d'
-        self.experiment = 'smfs'
-

     def _load_from_file(self, filename, extract_note=False):
         data = None
         f = open(filename, 'rb')
     def _load_from_file(self, filename, extract_note=False):
         data = None
         f = open(filename, 'rb')

diff --git a/hooke/driver/mfp1dexport.py b/hooke/driver/mfp1dexport.py
index 174696b04aa73333ee8e4dcb5c0d65836113e8b1..63f5851b6de1899ab0c78201a671f0cb461612dc 100644 (file)
--- a/hooke/driver/mfp1dexport.py
+++ b/hooke/driver/mfp1dexport.py
@@ -42,9 +42,6 @@ class mfp1dexportDriver(lhc.Driver):
         self.lines = list(self.filedata.readlines())
         self.filedata.close()
 
         self.lines = list(self.filedata.readlines())
         self.filedata.close()
 

-        self.filetype='mfp1dexport'
-        self.experiment='smfs'
-

     def close_all(self):
         self.filedata.close()
 
     def close_all(self):
         self.filedata.close()
 

diff --git a/hooke/driver/mfp3d.py b/hooke/driver/mfp3d.py
index 3347e3d0f863a5905b2ba983c16f061800154df5..cf71874338cc376dd1de8fd264b106ca89c6fe92 100644 (file)
--- a/hooke/driver/mfp3d.py
+++ b/hooke/driver/mfp3d.py
@@ -37,7 +37,6 @@ import pprint
 import numpy
 
 from .. import curve as curve
 import numpy
 
 from .. import curve as curve

-from .. import experiment as experiment

 from . import Driver as Driver
 from .igorbinarywave import loadibw
 
 from . import Driver as Driver
 from .igorbinarywave import loadibw
 


@@ -72,8 +71,6 @@ class MFP3DDriver (Driver):
     def read(self, path, info=None):
         data,bin_info,wave_info = loadibw(path)
         blocks,info = self._translate_ibw(data, bin_info, wave_info)
     def read(self, path, info=None):
         data,bin_info,wave_info = loadibw(path)
         blocks,info = self._translate_ibw(data, bin_info, wave_info)

-        info['filetype'] = self.name
-        info['experiment'] = experiment.VelocityClamp()

         return (blocks, info)
      
     def _translate_ibw(self, data, bin_info, wave_info):
         return (blocks, info)
      
     def _translate_ibw(self, data, bin_info, wave_info):

diff --git a/hooke/driver/picoforce.py b/hooke/driver/picoforce.py
index ca84792a3b470aef69afc1e9c99fc0f3b7518773..625c4555236e97b8632e2cc2fcf38504dcbb0ebd 100644 (file)
--- a/hooke/driver/picoforce.py
+++ b/hooke/driver/picoforce.py
@@ -29,7 +29,6 @@ import time
 import numpy
 
 from .. import curve as curve # this module defines data containers.
 import numpy
 
 from .. import curve as curve # this module defines data containers.

-from .. import experiment as experiment # this module defines expt. types

 from . import Driver as Driver # this is the Driver base class
 
 
 from . import Driver as Driver # this is the Driver base class
 
 


@@ -54,8 +53,6 @@ class PicoForceDriver (Driver):
         info = self._read_header_path(path)
         self._check_version(info)
         data = self._read_data_path(path, info)
         info = self._read_header_path(path)
         self._check_version(info)
         data = self._read_data_path(path, info)

-        info['filetype'] = self.name
-        info['experiment'] = experiment.VelocityClamp()

         return (data, info)
 
     def _read_header_path(self, path):
         return (data, info)
 
     def _read_header_path(self, path):

diff --git a/hooke/driver/tutorial.py b/hooke/driver/tutorial.py
index 6856f8dd3e05899545268c769d25e24c06eb2331..abd2dae39d793d73767ffc390175c08efcbc1acc 100644 (file)
--- a/hooke/driver/tutorial.py
+++ b/hooke/driver/tutorial.py
@@ -66,7 +66,6 @@ import os.path
 # The following are relative imports.  See PEP 328 for details
 #   http://www.python.org/dev/peps/pep-0328/
 from .. import curve as curve # this module defines data containers.
 # The following are relative imports.  See PEP 328 for details
 #   http://www.python.org/dev/peps/pep-0328/
 from .. import curve as curve # this module defines data containers.

-from .. import experiment as experiment # this module defines expt. types

 from ..config import Setting # configurable setting class
 from . import Driver as Driver # this is the Driver base class
 
 from ..config import Setting # configurable setting class
 from . import Driver as Driver # this is the Driver base class
 


@@ -136,5 +135,5 @@ class TutorialDriver (Driver):
         f.close() # remember to close the file
 
         data = curve.Data()
         f.close() # remember to close the file
 
         data = curve.Data()

-        info = {'filetype':'tutorial', 'experiment':experiment.Experiment()}
+        info = {}

         return (data, info)
         return (data, info)

diff --git a/hooke/driver/wtk.py b/hooke/driver/wtk.py
index 412470167bea5aa0635c0a0ec281fe8df43764f6..031fb80f98a1faa0144abb2e4540633d550cc490 100644 (file)
--- a/hooke/driver/wtk.py
+++ b/hooke/driver/wtk.py
@@ -42,7 +42,6 @@ import time
 import numpy
 
 from .. import curve as curve
 import numpy
 
 from .. import curve as curve

-from .. import experiment as experiment

 from ..config import Setting
 from . import Driver as Driver
 
 from ..config import Setting
 from . import Driver as Driver
 


@@ -98,7 +97,7 @@ class WTKDriver (Driver):
             unlabeled_approach_data, params, 'approach')
         retract = self._scale_block(
             unlabeled_retract_data, params, 'retract')
             unlabeled_approach_data, params, 'approach')
         retract = self._scale_block(
             unlabeled_retract_data, params, 'retract')

-        info = {'filetype':self.name, 'experiment':experiment.VelocityClamp()}
+        info = {}

         return ([approach, retract], info)
 
     def _paths(self, path):
         return ([approach, retract], info)
 
     def _paths(self, path):

diff --git a/hooke/experiment.py b/hooke/experiment.py
deleted file mode 100644 (file)
index 646b415..0000000
--- a/hooke/experiment.py
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright (C) 2010 W. Trevor King <wking@drexel.edu>
-#
-# This file is part of Hooke.
-#
-# Hooke is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as
-# published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# Hooke is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General
-# Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with Hooke.  If not, see
-# <http://www.gnu.org/licenses/>.
-
-"""Define :class:`Experiment` and assorted subclasses.
-
-This allows :class:`hooke.plugin.Plugin`\s to specify the types of
-experiments they can handle.
-"""
-
-from .util.singleton import Singleton
-
-
-class Experiment (Singleton):
-    """Base class for experiment classification.
-    """
-    pass
-
-class ForceClamp (Experiment):
-    """Constant force force spectroscopy [#fernandez2004]_.
-
-    .. [#fernandez2004] J.M. Fernandez, H. Li.
-      "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a
-      Single Protein."
-      Science, 2004.
-      doi: `10.1126/science.1092497 <http://dx.doi.org/10.1126/science.1092497>`_
-    """
-    pass
-
-class VelocityClamp (Experiment):
-    """Constant piezo velocity force spectroscopy [#rief1997]_.
-    
-    .. [#rief1997] M. Rief, M. Gautel, F. Oesterhelt, J.M. Fernandez,
-      H.E. Gaub.
-      "Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM."
-      Science, 1997.
-      doi: `10.1126/science.276.5315.1109 <http://dx.doi.org/10.1126/science.276.5315.1109>`_
-    """
-    pass
-
-class TwoColorCoincidenceDetection (Experiment):
-    """Two-color fluorescence coincidence spectroscopy [#clarke2007]_.
-
-    .. [#clarke2007] R.W. Clarke, A. Orte, D. Klenerman.
-      "Optimized Threshold Selection for Single-Molecule Two-Color
-      Fluorescence Coincidence Spectroscopy."
-      Anal. Chem., 2007.
-      doi: `10.1021/ac062188w <http://dx.doi.org/10.1021/ac062188w>`_
-    """
-    pass

diff --git a/hooke/plugin/convfilt.py b/hooke/plugin/convfilt.py
index a5780e98fdc25e2e670788138e54fa93e4429a9e..a741f69938ae223f06454546050c46aec1eef3b9 100644 (file)
--- a/hooke/plugin/convfilt.py
+++ b/hooke/plugin/convfilt.py
@@ -40,7 +40,6 @@ import numpy
 
 from ..command import Command, Argument, Success, Failure
 from ..config import Setting
 
 from ..command import Command, Argument, Success, Failure
 from ..config import Setting

-from ..experiment import VelocityClamp

 from ..util.fit import PoorFit
 from ..util.peak import find_peaks, find_peaks_arguments, Peak, _kwargs
 from . import Plugin, argument_to_setting
 from ..util.fit import PoorFit
 from ..util.peak import find_peaks, find_peaks_arguments, Peak, _kwargs
 from . import Plugin, argument_to_setting


@@ -149,9 +148,6 @@ class ConvolutionPeaksCommand (Command):
         deflection arrays.
         """
         curve = params['curve']
         deflection arrays.
         """
         curve = params['curve']

-        if not isinstance(curve.info['experiment'], VelocityClamp):
-            raise Failure('%s operates on VelocityClamp experiments, not %s'
-                          % (self.name, curve.info['experiment']))

         data = None
         for block in curve.data:
             if block.info['name'].startswith('retract'):
         data = None
         for block in curve.data:
             if block.info['name'].startswith('retract'):

diff --git a/hooke/plugin/curve.py b/hooke/plugin/curve.py
index dbdace99c68c73b88e3c0ac4a7d9ca0d3c1fb90f..3ef141ce0b14aa2d5d707f9108dccfd132c9e5cf 100644 (file)
--- a/hooke/plugin/curve.py
+++ b/hooke/plugin/curve.py
@@ -292,9 +292,8 @@ class InfoCommand (CurveCommand):
             Argument(name='all', type='bool', default=False, count=1,
                      help='Get all curve information.'),
             ]
             Argument(name='all', type='bool', default=False, count=1,
                      help='Get all curve information.'),
             ]

-        self.fields = ['name', 'path', 'experiment', 'driver', 'filetype',
-                       'note', 'command stack', 'blocks', 'block names',
-                       'block sizes']
+        self.fields = ['name', 'path', 'driver', 'note', 'command stack',
+                       'blocks', 'block names', 'block sizes']

         for field in self.fields:
             args.append(Argument(
                     name=field, type='bool', default=False, count=1,
         for field in self.fields:
             args.append(Argument(
                     name=field, type='bool', default=False, count=1,


@@ -326,15 +325,9 @@ class InfoCommand (CurveCommand):
     def _get_path(self, curve):
         return curve.path
 
     def _get_path(self, curve):
         return curve.path
 

-    def _get_experiment(self, curve):
-        return curve.info.get('experiment', None)
-

     def _get_driver(self, curve):
         return curve.driver
 
     def _get_driver(self, curve):
         return curve.driver
 

-    def _get_filetype(self, curve):
-        return curve.info.get('filetype', None)
-

     def _get_note(self, curve):
         return curve.info.get('note', None)
                               
     def _get_note(self, curve):
         return curve.info.get('note', None)
                               

diff --git a/hooke/plugin/flatfilt.py b/hooke/plugin/flatfilt.py
index 21665fecbc3e6412829deffdd39a123df69209f7..44f0e1f8ed3f5e1806e66cf4592a3516de924a3d 100644 (file)
--- a/hooke/plugin/flatfilt.py
+++ b/hooke/plugin/flatfilt.py
@@ -28,8 +28,7 @@ several associated :class:`~hooke.command.Command`\s for removing flat
 
 See Also
 --------
 
 See Also
 --------

-:mod:`~hooke.plugin.convfilt` for a convolution-based filter for
-:class:`~hooke.experiment.VelocityClamp` experiments.
+:mod:`~hooke.plugin.convfilt` for a convolution-based filter.

 """
 
 import copy
 """
 
 import copy


@@ -41,7 +40,6 @@ from scipy.signal.signaltools import medfilt
 from ..command import Argument, Success, Failure, UncaughtException
 from ..config import Setting
 from ..curve import Data
 from ..command import Argument, Success, Failure, UncaughtException
 from ..config import Setting
 from ..curve import Data

-from ..experiment import VelocityClamp

 from ..util.fit import PoorFit
 from ..util.peak import (find_peaks, peaks_to_mask,
                          find_peaks_arguments, Peak, _kwargs)
 from ..util.fit import PoorFit
 from ..util.peak import (find_peaks, peaks_to_mask,
                          find_peaks_arguments, Peak, _kwargs)


@@ -170,9 +168,6 @@ Name for storing the list of peaks in the `.info` dictionary.
         deflection arrays.
         """
         curve = self._curve(hooke=hooke, params=params)
         deflection arrays.
         """
         curve = self._curve(hooke=hooke, params=params)

-        if not isinstance(curve.info['experiment'], VelocityClamp):
-            raise Failure('%s operates on VelocityClamp experiments, not %s'
-                          % (self.name, curve.info['experiment']))

         for key,value in params.items():
             if value == None and key in self.plugin.config:
                 # Use configured default value.
         for key,value in params.items():
             if value == None and key in self.plugin.config:
                 # Use configured default value.