Added modular directory structure.

Also some import and other cleanups to convince myself that the
reorganization was mostly working.

diff --git a/CHANGELOG b/CHANGELOG
old mode 100755 (executable)
new mode 100644 (file)

diff --git a/bin/hooke b/bin/hooke
new file mode 100755 (executable)
index 0000000..5a57baa
--- /dev/null
+++ b/bin/hooke
@@ -0,0 +1,5 @@
+#!/usr/bin/python
+
+import hooke.hooke
+
+hooke.hooke.main()

diff --git a/conf/hooke.conf b/conf/hooke.conf
old mode 100755 (executable)
new mode 100644 (file)
index 75a31f9..c1d8d7b
--- a/conf/hooke.conf
+++ b/conf/hooke.conf
@@ -1,26 +1,59 @@
 <?xml version="1.0" ?>\r
 <!-- To comment something, put dashes and ! like here -->\r
 <config>\r
 <?xml version="1.0" ?>\r
 <!-- To comment something, put dashes and ! like here -->\r
 <config>\r

-<!-- Internal variabls. -->\r
-    <display ext="1" colour_ext="None" ret="1" colour_ret="None" correct="1" colour_correct="None" contact_point="0" medfilt="0" xaxes="0" yaxes="0" flatten="1" fit_function="wlc" temperature="301" auto_fit_points="50" auto_slope_span="20" auto_delta_force="10" auto_fit_nm="5" auto_min_p="0.005" auto_max_p="10" baseline_clicks="0" auto_left_baseline="20" auto_right_baseline="20" force_multiplier="1" fc_showphase="0" fc_showimposed="0" fc_interesting="0" tccd_threshold="0" tccd_coincident="0"/>\r

 \r
 \r

-<!-- \r
-The following section defines your own work directory. Substitute your work directory.\r
-     -->\r
-<workdir>\r
-    insert directory\r
-</workdir>\r
+\r
+<!--\r
+This section defines the Hooke installation.  confpath is hardcoded,\r
+since it's to find the config file(s) before your read them.\r
+    -->\r
+<install>\r
+    <docpath>\r
+        ./doc/\r
+    </docpath>\r
+</install>\r
+\r
+<!-- Internal variables. -->\r
+<display\r
+    ext="1"\r
+    colour_ext="None"\r
+    ret="1"\r
+    colour_ret="None"\r
+    correct="1"\r
+    colour_correct="None"\r
+    contact_point="0"\r
+    medfilt="0"\r
+    xaxes="0"\r
+    yaxes="0"\r
+    flatten="1"\r
+    fit_function="wlc"\r
+    temperature="301"\r
+    auto_fit_points="50"\r
+    auto_slope_span="20"\r
+    auto_delta_force="10"\r
+    auto_fit_nm="5"\r
+    auto_min_p="0.005"\r
+    auto_max_p="10"\r
+    baseline_clicks="0"\r
+    auto_left_baseline="20"\r
+    auto_right_baseline="20"\r
+    force_multiplier="1"\r
+    fc_showphase="0"\r
+    fc_showimposed="0"\r
+    fc_interesting="0"\r
+    tccd_threshold="0"\r
+    tccd_coincident="0"/>\r

 \r
 <!--\r
 The following section defines the default playlist to load at startup.\r
 \r
 <!--\r
 The following section defines the default playlist to load at startup.\r

--->\r
+    -->\r

 <defaultlist>\r
 <defaultlist>\r

-    test.hkp\r
+    ./hooke/test/test.hkp\r

 </defaultlist>\r
 \r
 <!--\r
 This section defines which plugins have to be loaded by Hooke.\r
 </defaultlist>\r
 \r
 <!--\r
 This section defines which plugins have to be loaded by Hooke.\r

-    -->\r
+     -->\r

 <plugins>\r
     <fit/>\r
     <procplots/>\r
 <plugins>\r
     <fit/>\r
     <procplots/>\r


@@ -69,4 +102,3 @@ and -IMPORTANTLY- their order.
 </plotmanips>\r
 \r
 </config>\r
 </plotmanips>\r
 \r
 </config>\r

-\r

diff --git a/conf/macro.conf b/conf/macro.conf
new file mode 100644 (file)
index 0000000..b197e36
--- /dev/null
+++ b/conf/macro.conf
@@ -0,0 +1,6 @@
+<?xml version="1.0" ?>
+<config>
+
+<!-- Set the location of your macros directory (for the macro plugin) -->
+<macrodir path="~/.hooke/macros" />
+</config>

diff --git a/doc/USAGE b/doc/USAGE
index 785f47d9f55117d52f6bb2f93f1b122e87ff0356..eed629a676202583ea98fb3354c9114f49d6b9b0 100644 (file)
--- a/doc/USAGE
+++ b/doc/USAGE
@@ -2,9 +2,9 @@ Starting Hooke
 ==============
 
 Open a terminal, go to the directory Hooke is installed and type
 ==============
 
 Open a terminal, go to the directory Hooke is installed and type

-python hooke/hooke.py (You may need to give the full path for Python
-on Windows systems).  If everything is OK, Hooke displays a nice
-splashscreen and starts.
+  python bin/hooke
+(You may need to give the full path for Python on Windows systems).
+If everything is OK, Hooke displays a nice splashscreen and starts.

 
 Once Hooke is launched from the terminal window, you see a text like
 the following:
 
 Once Hooke is launched from the terminal window, you see a text like
 the following:

diff --git a/doc/hooke.jpg b/doc/hooke.jpg
old mode 100755 (executable)
new mode 100644 (file)

diff --git a/hooke/__init__.py b/hooke/__init__.py
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/hooke/driver/__init__.py b/hooke/driver/__init__.py
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/hooke/driver/csvdriver.py b/hooke/driver/csvdriver.py
index fb465ee2c0083a6a0b251c9dc9da5f6464fc326e..1d05e232532eb67c9ecb1528dffa98f28550d179 100644 (file)
--- a/hooke/driver/csvdriver.py
+++ b/hooke/driver/csvdriver.py
@@ -12,8 +12,8 @@ If the number of columns is odd, the last column is ignored.
 (c)Massimo Sandal, 2008
 '''
 
 (c)Massimo Sandal, 2008
 '''
 

-import libhookecurve as lhc
-import libhooke as lh
+from .. import libhookecurve as lhc
+from .. import libhooke as lh

 import csv
 
 class csvdriverDriver(lhc.Driver):
 import csv
 
 class csvdriverDriver(lhc.Driver):

diff --git a/hooke/driver/hemingclamp.py b/hooke/driver/hemingclamp.py
old mode 100755 (executable)
new mode 100644 (file)
index 41e721a..3145404
--- a/hooke/driver/hemingclamp.py
+++ b/hooke/driver/hemingclamp.py
@@ -14,7 +14,7 @@ __changelog__='''
 2007_02_07: Initial implementation
 '''
 import string
 2007_02_07: Initial implementation
 '''
 import string

-import libhookecurve as lhc
+from .. import libhookecurve as lhc

 
 class DataChunk(list):
     '''Dummy class to provide ext and ret methods to the data list.
 
 class DataChunk(list):
     '''Dummy class to provide ext and ret methods to the data list.

diff --git a/hooke/driver/jpk.py b/hooke/driver/jpk.py
index 5fd5f5dae342ab591c0855c807ad603e5d9f3a10..090b09a25e30bf6e0badfe58e796a401f3eb6fe5 100644 (file)
--- a/hooke/driver/jpk.py
+++ b/hooke/driver/jpk.py
@@ -1,5 +1,5 @@
 import string
 import string

-import libhookecurve as lhc
+from .. import libhookecurve as lhc

 
 class DataChunk(list):
     #Dummy class to provide ext and ret methods to the data list.
 
 class DataChunk(list):
     #Dummy class to provide ext and ret methods to the data list.

diff --git a/hooke/driver/mcs.py b/hooke/driver/mcs.py
index 48836f2fb4b558506d89279b5342623957e7db3c..6562d90d1040510c80d7852005fd41aa7f3af86e 100644 (file)
--- a/hooke/driver/mcs.py
+++ b/hooke/driver/mcs.py
@@ -6,8 +6,8 @@ driver for mcs fluorescence files
 Massimo Sandal, Allen Chen (c) 2009
 '''
 
 Massimo Sandal, Allen Chen (c) 2009
 '''
 

-import libhookecurve as lhc
-import libhooke as lh
+from .. import libhookecurve as lhc
+from .. import libhooke as lh

 import struct
 
 class mcsDriver(lhc.Driver):
 import struct
 
 class mcsDriver(lhc.Driver):

diff --git a/hooke/driver/mfp1dexport.py b/hooke/driver/mfp1dexport.py
index 5cc18e53f7b25f10d2e3cb84c98bc57e7aa4f3ff..37af7df8e6fd022b61e026ad4e478b9252588a64 100644 (file)
--- a/hooke/driver/mfp1dexport.py
+++ b/hooke/driver/mfp1dexport.py
@@ -6,8 +6,8 @@ Driver for text-exported MFP 1D files
 Massimo Sandal (c) 2009
 '''
 
 Massimo Sandal (c) 2009
 '''
 

-import libhookecurve as lhc
-import libhooke as lh
+from .. import libhookecurve as lhc
+from .. import libhooke as lh

 
 class mfp1dexportDriver(lhc.Driver):
 
 
 class mfp1dexportDriver(lhc.Driver):
 

diff --git a/hooke/driver/picoforce.py b/hooke/driver/picoforce.py
old mode 100755 (executable)
new mode 100644 (file)
index e7df889..c60e57c
--- a/hooke/driver/picoforce.py
+++ b/hooke/driver/picoforce.py
@@ -11,7 +11,7 @@ This program is released under the GNU General Public License version 2.
 import re, struct
 from scipy import arange
 
 import re, struct
 from scipy import arange
 

-import libhookecurve as lhc
+from .. import libhookecurve as lhc

 
 __version__='0.0.0.20080404'
 
 
 __version__='0.0.0.20080404'
 

diff --git a/hooke/driver/picoforcealt.py b/hooke/driver/picoforcealt.py
index ec69118ecfd2d46217e82a3250438ec4d191b7cf..836fb4561cf89b0dc84a72516ed03bb02f7df332 100644 (file)
--- a/hooke/driver/picoforcealt.py
+++ b/hooke/driver/picoforcealt.py
@@ -12,7 +12,7 @@ This program is released under the GNU General Public License version 2.
 import re, struct
 from scipy import arange
 
 import re, struct
 from scipy import arange
 

-import libhookecurve as lhc
+from .. import libhookecurve as lhc

 
 __version__='0.0.0.20081706'
 
 
 __version__='0.0.0.20081706'
 

diff --git a/hooke/driver/tutorialdriver.py b/hooke/driver/tutorialdriver.py
index 9d38c476e9d9cf7ab78e5074b13dc800d5e81e58..8644eef97a8250c0e78cf9b423df989757337eac 100644 (file)
--- a/hooke/driver/tutorialdriver.py
+++ b/hooke/driver/tutorialdriver.py
@@ -45,7 +45,7 @@ END
 that is, two plots with two datasets each.
 '''
 
 that is, two plots with two datasets each.
 '''
 

-import libhookecurve as lhc #We need to import this library to define some essential data types
+from .. import libhookecurve as lhc #We need to import this library to define some essential data types

 
 class tutorialdriverDriver(lhc.Driver):
     '''
 
 class tutorialdriverDriver(lhc.Driver):
     '''

diff --git a/hooke/hooke.py b/hooke/hooke.py
old mode 100755 (executable)
new mode 100644 (file)
index 55f23b1..75cc7d9
--- a/hooke/hooke.py
+++ b/hooke/hooke.py
@@ -10,8 +10,7 @@ Copyright (C) 2008 Massimo Sandal (University of Bologna, Italy).
 This program is released under the GNU General Public License version 2.\r
 '''\r
 \r
 This program is released under the GNU General Public License version 2.\r
 '''\r
 \r

-from libhooke import HOOKE_VERSION\r
-from libhooke import WX_GOOD\r
+from .libhooke import HOOKE_VERSION, WX_GOOD\r

 \r
 import os\r
 \r
 \r
 import os\r
 \r


@@ -24,12 +23,12 @@ from wx.lib.newevent import NewEvent
 import matplotlib.numerix as nx\r
 import scipy as sp\r
 \r
 import matplotlib.numerix as nx\r
 import scipy as sp\r
 \r

-from threading import *\r
+from threading import Thread\r

 import Queue\r
 \r
 import Queue\r
 \r

-from hooke_cli import HookeCli\r
-from libhooke import *\r
-import libhookecurve as lhc\r
+from .hooke_cli import HookeCli\r
+from .libhooke import HookeConfig, ClickedPoint\r
+from . import libhookecurve as lhc\r

 \r
 #import file versions, just to know with what we're working...\r
 from hooke_cli import __version__ as hookecli_version\r
 \r
 #import file versions, just to know with what we're working...\r
 from hooke_cli import __version__ as hookecli_version\r


@@ -64,15 +63,20 @@ plugin_commands_namespaces=[]
 plugin_gui_namespaces=[]\r
 for plugin_name in config['plugins']:\r
     try:\r
 plugin_gui_namespaces=[]\r
 for plugin_name in config['plugins']:\r
     try:\r

-        plugin=__import__(plugin_name)\r
+        hooke_module=__import__('hooke.plugin.'+plugin_name)\r
+        plugin = getattr(hooke_module.plugin, plugin_name)\r

         try:\r
         try:\r

-            eval('CLI_PLUGINS.append(plugin.'+plugin_name+'Commands)') #take Command plugin classes\r
-            plugin_commands_namespaces.append(dir(eval('plugin.'+plugin_name+'Commands')))\r
+            #take Command plugin classes\r
+            commands = getattr(plugin, plugin_name+'Commands')\r
+            CLI_PLUGINS.append(commands)\r
+            plugin_commands_namespaces.append(dir(commands))\r

         except:\r
             pass\r
         try:\r
         except:\r
             pass\r
         try:\r

-            eval('GUI_PLUGINS.append(plugin.'+plugin_name+'Gui)') #take Gui plugin classes\r
-            plugin_gui_namespaces.append(dir(eval('plugin.'+plugin_name+'Gui')))\r
+            #take Gui plugin classes\r
+            gui = getattr(plugin, plugin_name+'Gui')\r
+            GUI_PLUGINS.append(gui)\r
+            plugin_gui_namespaces.append(dir(gui))\r

         except:\r
             pass\r
     except ImportError:\r
         except:\r
             pass\r
     except ImportError:\r


@@ -82,8 +86,11 @@ for plugin_name in config['plugins']:
         print 'Imported plugin ',plugin_name\r
 \r
 #eliminate names common to all namespaces\r
         print 'Imported plugin ',plugin_name\r
 \r
 #eliminate names common to all namespaces\r

-for i in range(len(plugin_commands_namespaces)):\r
-    plugin_commands_namespaces[i]=[item for item in plugin_commands_namespaces[i] if (item != '__doc__' and item != '__module__' and item != '_plug_init')]\r
+for i,namespace in enumerate(plugin_commands_namespaces):\r
+    plugin_commands_namespaces[i] = \\r
+        filter(lambda item : not (item.startswith('__')\r
+                                  or item == '_plug_init'),\r
+               namespace)\r

 #check for conflicts in namespaces between plugins\r
 #FIXME: only in commands now, because I don't have Gui plugins to check\r
 #FIXME: how to check for plugin-defined variables (self.stuff) ??\r
 #check for conflicts in namespaces between plugins\r
 #FIXME: only in commands now, because I don't have Gui plugins to check\r
 #FIXME: how to check for plugin-defined variables (self.stuff) ??\r


@@ -94,7 +101,8 @@ for namespace,plugin_name in zip(plugin_commands_namespaces, config['plugins']):
     for item in namespace:\r
         if item in plugin_commands_names:\r
             i=plugin_commands_names.index(item) #we exploit the fact index gives the *first* occurrence of a name...\r
     for item in namespace:\r
         if item in plugin_commands_names:\r
             i=plugin_commands_names.index(item) #we exploit the fact index gives the *first* occurrence of a name...\r

-            print 'Error. Plugin ',plugin_name,' defines a function already defined by ',whatplugin_defines[i],'!'\r
+            print 'Error. Plugin %s defines a function %s already defined by %s!' \\r
+                % (plugin_name, item, whatplugin_defines[i])\r

             print 'This should not happen. Please disable one or both plugins and contact the plugin authors to solve the conflict.'\r
             print 'Hooke cannot continue.'\r
             exit()\r
             print 'This should not happen. Please disable one or both plugins and contact the plugin authors to solve the conflict.'\r
             print 'Hooke cannot continue.'\r
             exit()\r


@@ -110,9 +118,10 @@ FILE_DRIVERS=[]
 LOADED_DRIVERS=[]\r
 for driver_name in config['drivers']:\r
     try:\r
 LOADED_DRIVERS=[]\r
 for driver_name in config['drivers']:\r
     try:\r

-        driver=__import__(driver_name)\r
+        hooke_module=__import__('hooke.driver.'+driver_name)\r
+        driver = getattr(hooke_module.driver, driver_name)\r

         try:\r
         try:\r

-            eval('FILE_DRIVERS.append(driver.'+driver_name+'Driver)')\r
+            FILE_DRIVERS.append(getattr(driver, driver_name+'Driver'))\r

         except:\r
             pass\r
     except ImportError:\r
         except:\r
             pass\r
     except ImportError:\r


@@ -353,7 +362,8 @@ class MainWindow(wx.Frame):
         #make sure we execute _plug_init() for every command line plugin we import\r
         for plugin_name in config['plugins']:\r
             try:\r
         #make sure we execute _plug_init() for every command line plugin we import\r
         for plugin_name in config['plugins']:\r
             try:\r

-                plugin=__import__(plugin_name)\r
+                hooke_module=__import__('hooke.plugin.'+plugin_name)\r
+                plugin = getattr(hooke_module.plugin, plugin_name)\r

                 try:\r
                     eval('plugin.'+plugin_name+'Gui._plug_init(self)')\r
                     pass\r
                 try:\r
                     eval('plugin.'+plugin_name+'Gui._plug_init(self)')\r
                     pass\r


@@ -760,7 +770,9 @@ class MySplashScreen(wx.SplashScreen):
         # This is a recipe to a the screen.\r
         # Modify the following variables as necessary.\r
         #aBitmap = wx.Image(name = "wxPyWiki.jpg").ConvertToBitmap()\r
         # This is a recipe to a the screen.\r
         # Modify the following variables as necessary.\r
         #aBitmap = wx.Image(name = "wxPyWiki.jpg").ConvertToBitmap()\r

-        aBitmap=wx.Image(name='hooke.jpg').ConvertToBitmap()\r
+        aBitmap=wx.Image(name=os.path.join(\r
+                config['install']['docpath'],\r
+                'hooke.jpg')).ConvertToBitmap()\r

         splashStyle = wx.SPLASH_CENTRE_ON_SCREEN | wx.SPLASH_TIMEOUT\r
         splashDuration = 2000 # milliseconds\r
         splashCallback = None\r
         splashStyle = wx.SPLASH_CENTRE_ON_SCREEN | wx.SPLASH_TIMEOUT\r
         splashDuration = 2000 # milliseconds\r
         splashCallback = None\r


@@ -783,16 +795,6 @@ class MySplashScreen(wx.SplashScreen):
 #------------------------------------------------------------------------------\r
 \r
 def main():\r
 #------------------------------------------------------------------------------\r
 \r
 def main():\r

-\r
-    #save the directory where Hooke is located\r
-    config['hookedir']=os.getcwd()\r
-\r
-    #now change to the working directory.\r
-    try:\r
-        os.chdir(config['workdir'])\r
-    except OSError:\r
-        print "Warning: Invalid work directory."\r
-\r

     app=wx.PySimpleApp()\r
 \r
     def make_gui_class(*bases):\r
     app=wx.PySimpleApp()\r
 \r
     def make_gui_class(*bases):\r


@@ -808,7 +810,6 @@ def main():
     my_cmdline=CliThread(main_frame, list_of_events)\r
     my_cmdline.start()\r
 \r
     my_cmdline=CliThread(main_frame, list_of_events)\r
     my_cmdline.start()\r
 \r

-\r

     app.MainLoop()\r
 \r
 if __name__ == '__main__':\r
     app.MainLoop()\r
 \r
 if __name__ == '__main__':\r

diff --git a/hooke/hooke_cli.py b/hooke/hooke_cli.py
old mode 100755 (executable)
new mode 100644 (file)
index fc0cee3..886563b
--- a/hooke/hooke_cli.py
+++ b/hooke/hooke_cli.py
@@ -10,14 +10,7 @@ Copyright (C) 2006 Massimo Sandal (University of Bologna, Italy).
 This program is released under the GNU General Public License version 2.
 '''
 
 This program is released under the GNU General Public License version 2.
 '''
 

-from libhooke import * #FIXME
-import libhookecurve as lhc
-
-import libinput as linp
-import liboutlet as lout
-
-from libhooke import WX_GOOD
-from libhooke import HOOKE_VERSION
+from .libhooke import HOOKE_VERSION, WX_GOOD

 
 import wxversion
 wxversion.select(WX_GOOD)
 
 import wxversion
 wxversion.select(WX_GOOD)


@@ -47,17 +40,19 @@ from numpy import __version__ as numpy_version
 from sys import version as python_version
 import platform
 
 from sys import version as python_version
 import platform
 

+from .libhooke import PlaylistXML
+from . import libhookecurve as lhc
+from . import libinput as linp
+from . import liboutlet as lout
+

 
 

-class HookeCli(cmd.Cmd):
+class HookeCli(cmd.Cmd, object):

 
     def __init__(self,frame,list_of_events,events_from_gui,config,drivers):
         cmd.Cmd.__init__(self)
 
         self.prompt = 'hooke: '
 
     def __init__(self,frame,list_of_events,events_from_gui,config,drivers):
         cmd.Cmd.__init__(self)
 
         self.prompt = 'hooke: '

-
-

         self.current_list=[] #the playlist we're using
         self.current_list=[] #the playlist we're using

-

         self.current=None    #the current curve under analysis.
         self.plots=None
         '''
         self.current=None    #the current curve under analysis.
         self.plots=None
         '''


@@ -71,8 +66,6 @@ class HookeCli(cmd.Cmd):
         then undergoes modifications by the plotmanip
         modifier functions. The modified plot is saved in self.plots and used if needed by other functions.
         '''
         then undergoes modifications by the plotmanip
         modifier functions. The modified plot is saved in self.plots and used if needed by other functions.
         '''

-
-

         self.pointer=0       #a pointer to navigate the current list
 
         #Things that come from outside
         self.pointer=0       #a pointer to navigate the current list
 
         #Things that come from outside


@@ -239,10 +232,11 @@ Syntax: loadlist [playlist file]
             self.current_list, self.playlist_generics=playxml.load(play_to_load)
             self.current_playxml=playxml
         except IOError:
             self.current_list, self.playlist_generics=playxml.load(play_to_load)
             self.current_playxml=playxml
         except IOError:

-            print 'File not found.'
+            print 'File not found.', play_to_load

             return
 
             return
 

-        print 'Loaded %s curves' %len(self.current_list)
+        print 'Loaded %s curves from %s' \
+            % (len(self.current_list), play_to_load)

 
         if 'pointer' in self.playlist_generics.keys():
             self.pointer=int(self.playlist_generics['pointer'])
 
         if 'pointer' in self.playlist_generics.keys():
             self.pointer=int(self.playlist_generics['pointer'])


@@ -514,8 +508,8 @@ Plots the current force curve
 Syntax: plot
         '''
     def do_plot(self,args):
 Syntax: plot
         '''
     def do_plot(self,args):

-
-        self.current.identify(self.drivers)
+        if self.current.identify(self.drivers) == False:
+            return

         self.plots=self.current.curve.default_plots()
         try:
             self.plots=self.current.curve.default_plots()
         self.plots=self.current.curve.default_plots()
         try:
             self.plots=self.current.curve.default_plots()

diff --git a/hooke/libhooke.py b/hooke/libhooke.py
old mode 100755 (executable)
new mode 100644 (file)
index 73534f2..05c9837
--- a/hooke/libhooke.py
+++ b/hooke/libhooke.py
@@ -10,8 +10,6 @@ With algorithms contributed by Francesco Musiani (University of Bologna, Italy)
 This program is released under the GNU General Public License version 2.
 '''
 
 This program is released under the GNU General Public License version 2.
 '''
 

-import libhookecurve as lhc
-

 import scipy
 import numpy
 import xml.dom.minidom
 import scipy
 import numpy
 import xml.dom.minidom


@@ -20,6 +18,8 @@ import os.path
 import string
 import csv
 
 import string
 import csv
 

+from . import libhookecurve as lhc
+

 HOOKE_VERSION=['0.8.3_devel', 'Seinei', '2008-04-16']
 WX_GOOD=['2.6','2.8']
 
 HOOKE_VERSION=['0.8.3_devel', 'Seinei', '2008-04-16']
 WX_GOOD=['2.6','2.8']
 


@@ -106,8 +106,13 @@ class PlaylistXML(object):
                 new_playlist=[]
                 for myfile in list_of_files:
                     #rebuild a data structure from the xml attributes
                 new_playlist=[]
                 for myfile in list_of_files:
                     #rebuild a data structure from the xml attributes

-                    the_curve=lhc.HookeCurve(myfile.getAttribute('path'))
-                    for attribute in myfile.attributes.keys(): #extract attributes for the single curve
+                    the_curve=lhc.HookeCurve(
+                        os.path.join(os.path.dirname(self.playpath),
+                                     myfile.getAttribute('path')))
+                    for attribute in myfile.attributes.keys():
+                        #extract attributes for the single curve
+                        if attribute == 'path':
+                            continue # we already added this attribute

                         the_curve.__dict__[attribute]=myfile.getAttribute(attribute)
                     new_playlist.append(the_curve)
 
                         the_curve.__dict__[attribute]=myfile.getAttribute(attribute)
                     new_playlist.append(the_curve)
 


@@ -129,6 +134,11 @@ class PlaylistXML(object):
             self.playlist.writexml(outfile,indent='\n')
             outfile.close()
 
             self.playlist.writexml(outfile,indent='\n')
             outfile.close()
 

+def config_file_path(filename, config_dir=None):
+    if config_dir == None:
+        config_dir = os.path.abspath(
+            os.path.join(os.path.dirname(os.path.dirname(__file__)), 'conf'))
+    return os.path.join(config_dir, filename)

 
 class HookeConfig(object):
     '''
 
 class HookeConfig(object):
     '''


@@ -142,18 +152,14 @@ class HookeConfig(object):
 
     def __init__(self, config_dir=None):
         self.config={}
 
     def __init__(self, config_dir=None):
         self.config={}

+        self.config['install']={}

         self.config['plugins']=[]
         self.config['drivers']=[]
         self.config['plotmanips']=[]
         self.config_dir = config_dir
         self.config['plugins']=[]
         self.config['drivers']=[]
         self.config['plotmanips']=[]
         self.config_dir = config_dir

-       if self.config_dir == None:
-            self.config_dir = os.path.abspath(
-               os.path.join(os.path.dirname(os.path.dirname(__file__)),
-                            'conf'))

 
     def load_config(self, filename):
 
     def load_config(self, filename):

-        print 'loading config file', os.path.join(self.config_dir, filename)
-        myconfig=file(os.path.join(self.config_dir, filename))
+        myconfig=file(config_file_path(filename, config_dir=self.config_dir))

 
         #the following 3 lines are needed to strip newlines. otherwise, since newlines
         #are XML elements too, the parser would read them (and re-save them, multiplying
 
         #the following 3 lines are needed to strip newlines. otherwise, since newlines
         #are XML elements too, the parser would read them (and re-save them, multiplying


@@ -175,19 +181,27 @@ class HookeConfig(object):
             return rc
 
         def handleConfig(config):
             return rc
 
         def handleConfig(config):

+            install_elements=config.getElementsByTagName("install")

             display_elements=config.getElementsByTagName("display")
             plugins_elements=config.getElementsByTagName("plugins")
             drivers_elements=config.getElementsByTagName("drivers")
             display_elements=config.getElementsByTagName("display")
             plugins_elements=config.getElementsByTagName("plugins")
             drivers_elements=config.getElementsByTagName("drivers")

-            workdir_elements=config.getElementsByTagName("workdir")

             defaultlist_elements=config.getElementsByTagName("defaultlist")
             plotmanip_elements=config.getElementsByTagName("plotmanips")
             defaultlist_elements=config.getElementsByTagName("defaultlist")
             plotmanip_elements=config.getElementsByTagName("plotmanips")

+            handleInstall(install_elements)

             handleDisplay(display_elements)
             handlePlugins(plugins_elements)
             handleDrivers(drivers_elements)
             handleDisplay(display_elements)
             handlePlugins(plugins_elements)
             handleDrivers(drivers_elements)

-            handleWorkdir(workdir_elements)

             handleDefaultlist(defaultlist_elements)
             handlePlotmanip(plotmanip_elements)
 
             handleDefaultlist(defaultlist_elements)
             handlePlotmanip(plotmanip_elements)
 

+        def handleInstall(install_elements):
+            for install in install_elements:
+                for node in install.childNodes:
+                    if node.nodeType == node.TEXT_NODE:
+                        continue
+                    path = os.path.abspath(getText(node.childNodes).strip())
+                    self.config['install'][str(node.tagName)] = path
+

         def handleDisplay(display_elements):
             for element in display_elements:
                 for attribute in element.attributes.keys():
         def handleDisplay(display_elements):
             for element in display_elements:
                 for attribute in element.attributes.keys():


@@ -214,13 +228,6 @@ class HookeConfig(object):
                 except: #if we allow fancy formatting of xml, there is a text node, so tagName fails for it...
                     pass
 
                 except: #if we allow fancy formatting of xml, there is a text node, so tagName fails for it...
                     pass
 

-        def handleWorkdir(workdir):
-            '''
-            default working directory
-            '''
-            wdir=getText(workdir[0].childNodes)
-            self.config['workdir']=wdir.strip()
-

         def handleDefaultlist(defaultlist):
             '''
             default playlist
         def handleDefaultlist(defaultlist):
             '''
             default playlist

diff --git a/hooke/libhookecurve.py b/hooke/libhookecurve.py
old mode 100755 (executable)
new mode 100644 (file)
index 0bb4a49..44dc9d6
--- a/hooke/libhookecurve.py
+++ b/hooke/libhookecurve.py
@@ -15,10 +15,8 @@ class HookeCurve(object):
                 #bring on all the driver, with his load of methods etc.
                 #so we can access the whole of it.
                 self.curve=tempcurve
                 #bring on all the driver, with his load of methods etc.
                 #so we can access the whole of it.
                 self.curve=tempcurve

-                del tempcurve

                 return True
                 return True

-
-        print 'Not a recognizable curve format.'
+        print 'Not a recognizable curve format: ', self.path

         return False
 
 
         return False
 
 

diff --git a/hooke/libviewer.py b/hooke/libviewer.py
index 5397a6e84cdd0edf1df9aec57346535edab8c698..f56160dc70cfaa4553c8aaf4024a8181e86e0eaa 100644 (file)
--- a/hooke/libviewer.py
+++ b/hooke/libviewer.py
@@ -19,8 +19,8 @@ and process it. Just a wrapper call for the specific one of each
 viewer. 
 '''
 
 viewer. 
 '''
 

-import liboutlet as lout
-import libinput as linput
+from . import liboutlet as lout
+from . import libinput as linput

 
 
 class Viewer(object):
 
 
 class Viewer(object):

diff --git a/hooke/plugin/__init__.py b/hooke/plugin/__init__.py
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/hooke/plugin/autopeak.py b/hooke/plugin/autopeak.py
index 17a30ed3120df8e21814f82fb336fa9cbdc451d3..bbea952e34cc5761b730f119dfdb919ca3b9b460 100644 (file)
--- a/hooke/plugin/autopeak.py
+++ b/hooke/plugin/autopeak.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 
 # -*- coding: utf-8 -*-
 

-from libhooke import WX_GOOD, ClickedPoint
+from hooke.libhooke import WX_GOOD, ClickedPoint
+

 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent
 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent

diff --git a/hooke/plugin/fit.py b/hooke/plugin/fit.py
old mode 100755 (executable)
new mode 100644 (file)
index 7ab6037..4b6ba7d
--- a/hooke/plugin/fit.py
+++ b/hooke/plugin/fit.py
@@ -7,13 +7,15 @@ Licensed under the GNU GPL version 2
 Non-standard Dependencies:
 procplots.py (plot processing plugin)
 '''
 Non-standard Dependencies:
 procplots.py (plot processing plugin)
 '''

-from libhooke import WX_GOOD, ClickedPoint
+from hooke.libhooke import WX_GOOD, ClickedPoint
+

 import wxversion
 wxversion.select(WX_GOOD)
 #from wx import PostEvent
 #from wx.lib.newevent import NewEvent
 import scipy
 import scipy.odr
 import wxversion
 wxversion.select(WX_GOOD)
 #from wx import PostEvent
 #from wx.lib.newevent import NewEvent
 import scipy
 import scipy.odr

+import scipy.stats

 import numpy as np
 import copy
 import Queue
 import numpy as np
 import copy
 import Queue

diff --git a/hooke/plugin/flatfilts.py b/hooke/plugin/flatfilts.py
old mode 100755 (executable)
new mode 100644 (file)
index 09dc3db..47eab59
--- a/hooke/plugin/flatfilts.py
+++ b/hooke/plugin/flatfilts.py
@@ -7,21 +7,20 @@ Licensed under the GNU LGPL version 2
 Other plugin dependencies:
 procplots.py (plot processing plugin)
 '''
 Other plugin dependencies:
 procplots.py (plot processing plugin)
 '''

-from libhooke import WX_GOOD
+
+from hooke.libhooke import WX_GOOD
+

 import wxversion
 wxversion.select(WX_GOOD)
 import wxversion
 wxversion.select(WX_GOOD)

-

 import xml.dom.minidom
 import xml.dom.minidom

-

 import wx
 import scipy
 import numpy
 from numpy import diff
 import wx
 import scipy
 import numpy
 from numpy import diff

-

 #import pickle
 
 #import pickle
 

-import libpeakspot as lps
-import libhookecurve as lhc
+from .. import libpeakspot as lps
+from .. import libhookecurve as lhc

 
 
 class flatfiltsCommands(object):
 
 
 class flatfiltsCommands(object):


@@ -29,14 +28,7 @@ class flatfiltsCommands(object):
     def _plug_init(self):
         #configurate convfilt variables
         convfilt_configurator=ConvfiltConfig()
     def _plug_init(self):
         #configurate convfilt variables
         convfilt_configurator=ConvfiltConfig()

-
-        #different OSes have different path conventions
-        if self.config['hookedir'][0]=='/':
-            slash='/' #a Unix or Unix-like system
-        else:
-            slash='\\' #it's a drive letter, we assume it's Windows
-
-        self.convfilt_config=convfilt_configurator.load_config(self.config['hookedir']+slash+'convfilt.conf')
+        self.convfilt_config=convfilt_configurator.load_config('convfilt.conf')

 
     def do_flatfilt(self,args):
         '''
 
     def do_flatfilt(self,args):
         '''

diff --git a/hooke/plugin/generalclamp.py b/hooke/plugin/generalclamp.py
index e3c6fe1c2e3fc05fa9dcaa8ab5139b0e12c660dc..2777f499e8cb1605630fb330a1d98a390411f574 100644 (file)
--- a/hooke/plugin/generalclamp.py
+++ b/hooke/plugin/generalclamp.py
@@ -3,12 +3,15 @@ GENERALCLAMP.py
 
 Plugin regarding general force clamp measurements
 '''
 
 Plugin regarding general force clamp measurements
 '''

-from libhooke import WX_GOOD, ClickedPoint
+from hooke.libhooke import WX_GOOD, ClickedPoint
+

 import wxversion
 import wxversion

-import libhookecurve as lhc

 wxversion.select(WX_GOOD)
 from wx import PostEvent
 
 wxversion.select(WX_GOOD)
 from wx import PostEvent
 

+from .. import libhookecurve as lhc
+
+

 class generalclampCommands(object):
 
     def plotmanip_clamp(self, plot, current, customvalue=False):
 class generalclampCommands(object):
 
     def plotmanip_clamp(self, plot, current, customvalue=False):

diff --git a/hooke/plugin/generalvclamp.py b/hooke/plugin/generalvclamp.py
index 28131503c3c96c3b400a8b72dd2010cec9385064..45cfa2c41d18e3199eb6cc8388aef02ce6a2fa13 100644 (file)
--- a/hooke/plugin/generalvclamp.py
+++ b/hooke/plugin/generalvclamp.py
@@ -4,7 +4,7 @@ generalvclamp.py
 Plugin regarding general velocity clamp measurements
 '''
 
 Plugin regarding general velocity clamp measurements
 '''
 

-from libhooke import WX_GOOD, ClickedPoint
+from hooke.libhooke import WX_GOOD, ClickedPoint

 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent
 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent

diff --git a/hooke/plugin/macro.py b/hooke/plugin/macro.py
index 88d13a50b654adba3e7b1c01f6a9f7987182c204..2a1ca997aea3c1b6a8dad635d7168d6779990b27 100644 (file)
--- a/hooke/plugin/macro.py
+++ b/hooke/plugin/macro.py
@@ -5,17 +5,18 @@ Records, saves and executes batches of commands
 (c)Alberto Gomez-Casado 2008
 '''
 
 (c)Alberto Gomez-Casado 2008
 '''
 

-import libhookecurve as lhc
-import libinput as linput

 import os.path
 import string
 
 import os.path
 import string
 

+from .. import libhookecurve as lhc
+from .. import libinput as linput
+

 class macroCommands(object):
 
        currentmacro=[]
        pause=0
        auxprompt=[]
 class macroCommands(object):
 
        currentmacro=[]
        pause=0
        auxprompt=[]

-       macrodir=[]
+       macrodir=None

        
 
        def _plug_init(self):
        
 
        def _plug_init(self):

diff --git a/hooke/plugin/massanalysis.py b/hooke/plugin/massanalysis.py
index 0a36657ff996a4c7d1678b02d84babe242cd6d58..a9ea6155361c4c102964f1c67cd99150e3f8e23a 100644 (file)
--- a/hooke/plugin/massanalysis.py
+++ b/hooke/plugin/massanalysis.py
@@ -8,14 +8,13 @@ libpeakspot.py
 flatfilts.py
 '''
 
 flatfilts.py
 '''
 

-
-import libpeakspot as lps
-import libhookecurve as lhc
-import libhooke as lh

 import numpy as np
 import numpy as np

-

 import csv
 
 import csv
 

+from .. import libpeakspot as lps
+from .. import libhookecurve as lhc
+from .. import libhooke as lh
+

 class massanalysisCommands(object):
 
     def _plug_init(self):
 class massanalysisCommands(object):
 
     def _plug_init(self):

diff --git a/hooke/plugin/multidistance.py b/hooke/plugin/multidistance.py
index 517a286ad638aa66b5379ec3c7571b019c3883f7..9db5f5dc969c2dd657389f2bb00b0ef9f4231d6f 100644 (file)
--- a/hooke/plugin/multidistance.py
+++ b/hooke/plugin/multidistance.py
@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 # -*- coding: utf-8 -*-

-from libhooke import WX_GOOD, ClickedPoint
+from hooke.libhooke import WX_GOOD, ClickedPoint
+

 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent
 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent

diff --git a/hooke/plugin/pcluster.py b/hooke/plugin/pcluster.py
index 2e166201dbf13f051e40e21fa846f09bafde2388..eb1770a564815bde3ed10ff1ad4c579e90cc72b5 100644 (file)
--- a/hooke/plugin/pcluster.py
+++ b/hooke/plugin/pcluster.py
@@ -1,5 +1,6 @@
+from ..libhooke import WX_GOOD, ClickedPoint, config_file_path
+

 from mdp import pca
 from mdp import pca

-from libhooke import WX_GOOD, ClickedPoint

 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent
 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent


@@ -8,9 +9,11 @@ import scipy as sp
 import copy
 import os.path
 import time
 import copy
 import os.path
 import time

-import libhookecurve as lhc

 import pylab as pyl
 
 import pylab as pyl
 

+from .. import libhookecurve as lhc
+
+

 import warnings
 warnings.simplefilter('ignore',np.RankWarning)
 
 import warnings
 warnings.simplefilter('ignore',np.RankWarning)
 


@@ -28,13 +31,9 @@ class pclusterCommands(object):
         Automatically measures peaks and extracts informations for further clustering
         (c)Paolo Pancaldi, Massimo Sandal 2009
         '''
         Automatically measures peaks and extracts informations for further clustering
         (c)Paolo Pancaldi, Massimo Sandal 2009
         '''

-        if self.config['hookedir'][0]=='/':
-            slash='/' #a Unix or Unix-like system
-        else:
-            slash='\\'

         blindw = str(self.convfilt_config['blindwindow'])
         pclus_dir = "pCluster_blind"+blindw+"_"+time.strftime("%Y%m%d_%H%M")
         blindw = str(self.convfilt_config['blindwindow'])
         pclus_dir = "pCluster_blind"+blindw+"_"+time.strftime("%Y%m%d_%H%M")

-        self.my_work_dir = os.getcwd()+slash+pclus_dir+slash
+        self.my_work_dir = os.path.join(os.getcwd(), pclus_dir)

         self.my_curr_dir = os.path.basename(os.getcwd())
         os.mkdir(self.my_work_dir)
 
         self.my_curr_dir = os.path.basename(os.getcwd())
         os.mkdir(self.my_work_dir)
 


@@ -343,14 +342,7 @@ class pclusterCommands(object):
         '''
 
         # reads the columns of pca
         '''
 
         # reads the columns of pca

-        if self.config['hookedir'][0]=='/':
-            slash='/' #a Unix or Unix-like system
-        else:
-            slash='\\'
-        self.my_hooke_dir = self.config['hookedir']+slash
-        #self.my_work_dir = os.getcwd()+slash+"pCluster_"+time.strftime("%Y%m%d_%H%M")+slash
-        #self.my_curr_dir = os.path.basename(os.getcwd())
-        conf=open(self.my_hooke_dir+"pca_config.txt")
+        conf=open(config_file_path("pca_config.txt"), 'r')

         config = conf.readlines()
         conf.close()
 
         config = conf.readlines()
         conf.close()
 

diff --git a/hooke/plugin/procplots.py b/hooke/plugin/procplots.py
old mode 100755 (executable)
new mode 100644 (file)
index 612ae0b..b8baa15
--- a/hooke/plugin/procplots.py
+++ b/hooke/plugin/procplots.py
@@ -4,17 +4,19 @@ Processed plots plugin for force curves.
 
 Licensed under the GNU GPL version 2
 '''
 
 Licensed under the GNU GPL version 2
 '''

-from libhooke import WX_GOOD
+from ..libhooke import WX_GOOD

 import wxversion
 wxversion.select(WX_GOOD)
 
 import wx
 import wxversion
 wxversion.select(WX_GOOD)
 
 import wx

-import libhookecurve as lhc

 import numpy as np
 import scipy as sp
 import scipy.signal
 import copy
 
 import numpy as np
 import scipy as sp
 import scipy.signal
 import copy
 

+from .. import libhookecurve as lhc
+
+

 class procplotsCommands(object):
 
     def _plug_init(self):
 class procplotsCommands(object):
 
     def _plug_init(self):

diff --git a/hooke/plugin/superimpose.py b/hooke/plugin/superimpose.py
index 41083f68651f0f9a03d7fd16b856d19e6c950759..448ded342d687a2563ee1456c32449b00cb0dd0b 100644 (file)
--- a/hooke/plugin/superimpose.py
+++ b/hooke/plugin/superimpose.py
@@ -1,11 +1,11 @@
-from libhooke import WX_GOOD
+from ..libhooke import WX_GOOD

 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent
 import wxversion
 wxversion.select(WX_GOOD)
 from wx import PostEvent

-
-import libhookecurve as lhc

 from numpy import arange, mean
 
 from numpy import arange, mean
 

+from .. import libhookecurve as lhc
+

 class superimposeCommands(object):
 
     def _plug_init(self):
 class superimposeCommands(object):
 
     def _plug_init(self):

diff --git a/hooke/plugin/tutorial.py b/hooke/plugin/tutorial.py
old mode 100755 (executable)
new mode 100644 (file)
index 50a0d78..61461f6
--- a/hooke/plugin/tutorial.py
+++ b/hooke/plugin/tutorial.py
@@ -6,10 +6,10 @@ internals.
 (c)Massimo Sandal 2007
 '''
 
 (c)Massimo Sandal 2007
 '''
 

-import libhookecurve as lhc
-

 import numpy as np
 
 import numpy as np
 

+from .. import libhookecurve as lhc
+

 '''
 SYNTAX OF DATA TYPE DECLARATION:
     type = type of object
 '''
 SYNTAX OF DATA TYPE DECLARATION:
     type = type of object

diff --git a/hooke/plugin/viewer.py b/hooke/plugin/viewer.py
index 7a6881dd25e4c7a81adb3322e705090a389ebf64..43f74aee2d5404201818586ce8ca7b32f463e4f2 100644 (file)
--- a/hooke/plugin/viewer.py
+++ b/hooke/plugin/viewer.py
@@ -7,8 +7,8 @@ This program is released under the GNU General Public License version 2.
 '''
 
 
 '''
 
 

-import libviewer as lview
-import libinput as linput
+from .. import libviewer as lview
+from .. import libinput as linput

 
 class viewerCommands(object):
        
 
 class viewerCommands(object):
        

diff --git a/hooke/test/default.000 b/hooke/test/default.000
old mode 100755 (executable)
new mode 100644 (file)

diff --git a/hooke/test/test.hkp b/hooke/test/test.hkp
index da648f4f031df7e7cdfaa0343502d04214c7aa7d..883d5976e0fa12a4dd26a74199630167d28fa037 100644 (file)
--- a/hooke/test/test.hkp
+++ b/hooke/test/test.hkp
@@ -2,4 +2,4 @@
 <playlist>
 <generics pointer="0"/>
 <element notes="" path="default.000"/>
 <playlist>
 <generics pointer="0"/>
 <element notes="" path="default.000"/>

-</playlist>
\ No newline at end of file
+</playlist>