Merge pull request #8 from ePSIC-DLS/master

Update branch

docs/getting_started.rst

@@ -0,0 +1,3 @@
+.. _getting_started:
+
+Work in progress.

docs/index.rst

@@ -9,6 +9,8 @@ Welcome to epsic_tools's documentation!
 .. toctree::
    :maxdepth: -1
    :caption: Contents:
+
+   getting_started.rst
 
 
 Indices and tables

docs/source/epsic_tools.rst

@@ -0,0 +1,46 @@
+epsic\_tools package
+====================
+
+Subpackages
+-----------
+
+.. toctree::
+
+   epsic_tools.signals
+   epsic_tools.toolbox
+
+Submodules
+----------
+
+epsic\_tools.api module
+-----------------------
+
+.. automodule:: epsic_tools.api
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epsic\_tools.build\_params module
+---------------------------------
+
+.. automodule:: epsic_tools.build_params
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epsic\_tools.ptychography2D module
+----------------------------------
+
+.. automodule:: epsic_tools.ptychography2D
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: epsic_tools
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/epsic_tools.signals.rst

@@ -0,0 +1,10 @@
+epsic\_tools.signals package
+============================
+
+Module contents
+---------------
+
+.. automodule:: epsic_tools.signals
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/epsic_tools.toolbox.rst

@@ -0,0 +1,70 @@
+epsic\_tools.toolbox package
+============================
+
+Submodules
+----------
+
+epsic\_tools.toolbox.define\_probe\_function module
+---------------------------------------------------
+
+.. automodule:: epsic_tools.toolbox.define_probe_function
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epsic\_tools.toolbox.make\_merlin\_mask module
+----------------------------------------------
+
+.. automodule:: epsic_tools.toolbox.make_merlin_mask
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epsic\_tools.toolbox.make\_merlin\_mask\_test module
+----------------------------------------------------
+
+.. automodule:: epsic_tools.toolbox.make_merlin_mask_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epsic\_tools.toolbox.ptycho\_utils module
+-----------------------------------------
+
+.. automodule:: epsic_tools.toolbox.ptycho_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epsic\_tools.toolbox.radial\_profile module
+-------------------------------------------
+
+.. automodule:: epsic_tools.toolbox.radial_profile
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epsic\_tools.toolbox.sim\_utils module
+--------------------------------------
+
+.. automodule:: epsic_tools.toolbox.sim_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+epsic\_tools.toolbox.warp\_3d module
+------------------------------------
+
+.. automodule:: epsic_tools.toolbox.warp_3d
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: epsic_tools.toolbox
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/modules.rst

@@ -0,0 +1,7 @@
+epsic_tools
+===========
+
+.. toctree::
+   :maxdepth: 4
+
+   epsic_tools

epsic_tools/build_params.py

@@ -151,6 +151,8 @@ def init_ptyrex():
     params['process']['common']['scan']['dR'] = [1e-11, 1e-11]
 
     params['process']['common']['scan']['N'] = [64,64]
+
+    params['process']['common']['scan']['region'] = [0.0 , 1.0, 0.0, 1.0, 1, 1]
 
 
 

epsic_tools/ptychography2D.py

@@ -126,6 +126,16 @@ def set_save_interval(self, val):
 
     def get_iterations(self):
         return self.ptyrex['process']['PIE']['iterations']
+
+    def get_scan_refine_start(self):
+        return self.ptyrex['process']['PIE']['scan']['start']
+
+    def set_scan_refine_start(self, val):
+        if int(val) == val:
+            self.ptyrex['process']['PIE']['scan']['start'] = val
+        else:
+            raise ValueError("scan refine start must be an integer")
+
 
     def get_decay(self):
         return self.ptyrex['process']['PIE']['decay']
@@ -226,9 +236,29 @@ def set_load_probe_path(self, val):
         else:
             raise ValueError("probe path must be a string")
 
+    def get_probe_start(self):
+        return self.ptyrex['process']['PIE']['probe']['start']
+
+    def set_probe_start(self, val):
+        #todo : check if path is valid here??
+        if is_number(val) == True:
+            self.ptyrex['process']['PIE']['probe']['start'] = val
+        else:
+            raise ValueError("probe start must be a number")
+
+    def get_probe_alpha(self):
+        return self.ptyrex['process']['PIE']['probe']['alpha']
+
+    def set_probe_alpha(self, val):
+        #todo : check if path is valid here??
+        if is_number(val) == True:
+            self.ptyrex['process']['PIE']['probe']['alpha'] = val
+        else:
+            raise ValueError("probe alpha must be a number")
+
     def get_load_object_flag(self):
         return self.ptyrex['process']['common']['object']['load_flag']
-        
+
     def set_load_object_flag(self, val):
         if val == 1 or val == 0:
             self.ptyrex['process']['common']['object']['load_flag'] = val
@@ -270,7 +300,19 @@ def set_scan_size(self, val):
             self.ptyrex['process']['common']['scan']['N'] = val
         else:
             raise ValueError("scan size must take the form [x, y]")
-
+
+    def set_scan_region(self, val):
+    #scan region must take the form [x_start,x_end, y_start, y_end, x_step, y_step]
+    #start 0.0 = first px
+    #end 1.0 = last px
+        if len(val) == 6:
+            self.ptyrex['process']['common']['scan']['region'] = val
+        else:
+            raise ValueError("scan region must take the form [x_start,x_end, y_start, y_end, x_step, y_step]")
+
+    def get_scan_region(self, val):
+        return self.ptyrex['process']['common']['scan']['region']
+
     def get_load_data_flag(self):
         return self.ptyrex['experiment']['data']['load_flag']