Debug for calculating atom number.

Add selecting the effective area function in AbsorptionImaging.py.

Optimaze plotting function.

.idea/workspace.xml

@@ -1,7 +1,11 @@
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+      <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/dylab/AbsorptionImaging.py" beforeDir="false" afterPath="$PROJECT_DIR$/dylab/AbsorptionImaging.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/test_absorption_imaging.py" beforeDir="false" afterPath="$PROJECT_DIR$/test_absorption_imaging.py" afterDir="false" />
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@@ -14,6 +18,9 @@
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+      <option name="project" value="LOCAL" />
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@@ -89,6 +120,10 @@
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+        <line-breakpoint enabled="true" suspend="THREAD" type="python-line">
+          <url>file://$PROJECT_DIR$/test_absorption_imaging.py</url>
+          <option name="timeStamp" value="56" />
+        </line-breakpoint>
       </breakpoints>
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dylab.egg-info/PKG-INFO

@@ -1,17 +0,0 @@
-Metadata-Version: 2.1
-Name: dylab
-Version: 0.0.1
-Summary: An internal toolbox package used for analyzation data of an ultracold atom experiment.
-Home-page: UNKNOWN
-Author: QF-group (AG Chomaz), Heidelberg university
-Author-email: gao@physi.uni-heidelberg.de
-License: UNKNOWN
-Platform: UNKNOWN
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Operating System :: OS Independent
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-UNKNOWN
-

dylab.egg-info/SOURCES.txt

@@ -1,14 +0,0 @@
-LICENSE
-README.md
-setup.py
-dylab/AbsorptionImaging.py
-dylab/Camera.py
-dylab/DyTransition.py
-dylab/Fitting.py
-dylab/FittingFunction.py
-dylab/TransitionClass.py
-dylab/__init__.py
-dylab.egg-info/PKG-INFO
-dylab.egg-info/SOURCES.txt
-dylab.egg-info/dependency_links.txt
-dylab.egg-info/top_level.txt

dylab.egg-info/dependency_links.txt

@@ -1 +0,0 @@
-

dylab.egg-info/top_level.txt

@@ -1 +0,0 @@
-dylab

dylab/AbsorptionImaging.py

@@ -52,6 +52,13 @@ class absorption_imaging:
         self.image_dark = None
         self.image_absorption = None
 
+        #
+        self.image_absorption_cut = None
+        self.x_start = None
+        self.y_start = None
+        self.x_end = None
+        self.y_end = None
+
         # import the data of transition
         # The transition should be an object of TransitionClass.py in module TransitionConstant
         # self.transition = transition
@@ -93,10 +100,6 @@ class absorption_imaging:
         self.image_background = self.image_background.astype(float)
         self.image_dark = self.image_dark.astype(float)
 
-        if not (self.intensity is None):
-            intensity = np.ones(self.image_atoms.shape)
-            self.intensity = intensity * self.intensity
-
     def close(self):
         self.save()
 
@@ -107,6 +110,19 @@ class absorption_imaging:
         if self.atom_number is not None:
             self.data_handle.save_result('atom_number', self.atom_number, 'results/absorption_imaging/')
 
+    # select the effective data in an rectangle area defined by coordinates of two conner
+    # The select region will be presented as a red box in the plotting
+    def select_effective_data(self, left_up_conner, right_down_conner):
+
+        self.x_start = left_up_conner[0]
+        self.x_end = right_down_conner[0]
+        self.y_start = left_up_conner[1]
+        self.y_end = right_down_conner[1]
+
+        self.image_absorption_cut = self.image_absorption[self.y_start:self.y_end, self.x_start:self.x_end]
+
+        return self.image_absorption_cut
+
     # The function do the analyzation for absorption imaging
     # It will return a two-dimensional array, which stores the absorption imaging
     def get_image_absorption(self):
@@ -155,14 +171,22 @@ class absorption_imaging:
         if self.atom_number is not None and not force_to_run:
             return self.atom_number
 
-        if self.image_absorption is None and not force_to_run:
+        if self.image_absorption is None or not force_to_run:
             self.image_absorption = self.get_image_absorption()
 
-        OD_act = self.image_absorption
+        if self.image_absorption_cut is None:
+            self.image_absorption_cut = self.image_absorption
+            self.x_start = 0
+            self.x_end = self.image_absorption.shape[1]
+            self.y_start = 0
+            self.y_end = self.image_absorption.shape[0]
+
+        OD_act = self.image_absorption_cut
 
         cross_section = self.transition.get_cross_section(self.detuning, self.intensity)
 
-        self.atom_number = np.sum(cross_section * OD_act) * self.camera['pixel_size_V'] * self.camera['pixel_size_H']
+        self.atom_number = np.sum(1 / cross_section * OD_act) * self.camera['pixel_size_V'] * self.camera[
+            'pixel_size_H']
 
         return self.atom_number
 
@@ -171,7 +195,7 @@ class absorption_imaging:
 
         cmap = plt.cm.get_cmap("jet")
 
-        grid = plt.GridSpec(3, 3, wspace=0.2, hspace=0.2)
+        grid = plt.GridSpec(3, 3, wspace=0.3, hspace=0.3)
 
         ax1 = plt.subplot(grid[0, 0])
         pos = ax1.imshow(self.image_atoms, cmap=cmap)
@@ -188,9 +212,19 @@ class absorption_imaging:
         ax3.set_title('Dark')
         plt.colorbar(pos, ax=ax3)
 
-        ax4 = plt.subplot(grid[0:3, 1:3])
+        ax4 = plt.subplot(grid[0:2, 1:3])
         pos = ax4.imshow(self.image_absorption, cmap=cmap, vmin=vmin, vmax=vmax)
         ax4.set_title('Absorption Imaging')
         plt.colorbar(pos, ax=ax4)
+        ax4.plot([self.x_start, self.x_start], [self.y_start, self.y_end], color='black')
+        ax4.plot([self.x_end, self.x_end], [self.y_start, self.y_end], color='black')
+        ax4.plot([self.x_start, self.x_end], [self.y_start, self.y_start], color='black')
+        ax4.plot([self.x_start, self.x_end], [self.y_end, self.y_end], color='black')
+
+        ax5 = plt.subplot(grid[2:3, 1:3])
+        atom_number_str = '{:g}'.format(self.atom_number)
+        ax5.text(0, 0.55, 'Atom Number : '+atom_number_str, horizontalalignment='left', verticalalignment='center',
+                 transform=ax5.transAxes, fontsize=40)
+        plt.axis('off')
 
         plt.show()

test_absorption_imaging.py

@@ -8,6 +8,7 @@ mot_3D_camera = Camera.c11440_36u(absorption_imaging_transition['wavelength'])
 with AbsorptionImaging.absorption_imaging(path, 'MOT_3D_Camera', 'in_situ_absorption',
                                           absorption_imaging_transition, mot_3D_camera, 0, 0) as absorption_image:
 
-    absorption_image.plot_result(-0.05, 0.03)
+    absorption_image.select_effective_data((800, 500), (1000, 700))
+    absorption_image.plot_result(-0.05, 0.05)
 
     print(absorption_image.atom_number)