Fix problems with the transition to the new nested-Config h5config package.

Also restore BumpConfig's `initial-position` setting, since it's
critical to running a bump.  I removed it when I mistakenly thought it
was storeing the output voltage used as the initial position
(something that you'd measure during a bump).  I guess I should have
read the help string before I deleted it ;).

There are also a number of numpy array -> float conversions when
loading HDF5.  This avoids excessive numpy-fication with h5py v2.0.

diff --git a/calibcant/T_analyze.py b/calibcant/T_analyze.py
index d03bf4d505ce7585b2049e883ececa0ab64a3edf..f7a92e3662ed188a2fe91dbbfed364eca087ebbd 100644 (file)
--- a/calibcant/T_analyze.py
+++ b/calibcant/T_analyze.py
@@ -115,9 +115,10 @@ def T_save(filename, group='/', raw_T=None, temperature_config=None,
             except KeyError:
                 pass
             cwg['raw'] = raw_T
             except KeyError:
                 pass
             cwg['raw'] = raw_T

-        if temperature_config:
+        if temperature_config is not None:

             config_cwg = _h5_create_group(cwg, 'config')
             config_cwg = _h5_create_group(cwg, 'config')

-            temperature_config.save(group=config_cwg)
+            storage = _HDF5_Storage()
+            storage.save(config=temperature_config, group=config_cwg)

         if processed_T is not None:
             try:
                 del cwg['processed']
         if processed_T is not None:
             try:
                 del cwg['processed']

diff --git a/calibcant/analyze.py b/calibcant/analyze.py
index e29d6c70f0fb016ada5356b35d6f844352445da9..dcfc7471304426f2b58df0b23e182f9860859e9f 100644 (file)
--- a/calibcant/analyze.py
+++ b/calibcant/analyze.py
@@ -234,7 +234,8 @@ def calib_save(filename, group='/', bumps=None, temperatures=None,
         cwg = _h5_create_group(f, group)
         if calibration_config is not None:
             config_cwg = _h5_create_group(cwg, 'config')
         cwg = _h5_create_group(f, group)
         if calibration_config is not None:
             config_cwg = _h5_create_group(cwg, 'config')

-            calibration_config.save(group=config_cwg)
+            storage = _HDF5_Storage()
+            storage.save(config=calibration_config, group=config_cwg)

         if bumps is not None:
             try:
                 del cwg['raw/photodiode-sensitivity/data']
         if bumps is not None:
             try:
                 del cwg['raw/photodiode-sensitivity/data']


@@ -304,11 +305,12 @@ def calib_load(filename, group='/'):
         except KeyError:
             pass
         try:
         except KeyError:
             pass
         try:

-            k = f[group+'processed/spring-constant/data'][...]
+            k = float(f[group+'processed/spring-constant/data'][...])

         except KeyError:
             pass
         try:
         except KeyError:
             pass
         try:

-            k_s = f[group+'processed/spring-constant/standard-deviation'][...]
+            k_s = float(
+                f[group+'processed/spring-constant/standard-deviation'][...])

         except KeyError:
             pass
     calibration_config = _CalibrationConfig(storage=_HDF5_Storage(
         except KeyError:
             pass
     calibration_config = _CalibrationConfig(storage=_HDF5_Storage(


@@ -345,13 +347,12 @@ def calib_load_all(filename, group='/'):
         filename, group+'calibration/')
     bump_details = []
     for i in range(calibration_config['num-bumps']):
         filename, group+'calibration/')
     bump_details = []
     for i in range(calibration_config['num-bumps']):

-        (raw_bump,bump_config,z_channel_config,z_axis_config,
-         deflection_channel_config,processed_bump) = _bump_load(
+        (raw_bump,bump_config,z_axis_config,deflection_channel_config,
+         processed_bump) = _bump_load(

             filename=filename, group='%sbump/%d/' % (group, i))
         bump_details.append({
                 'raw_bump': raw_bump,
                 'bump_config': bump_config,
             filename=filename, group='%sbump/%d/' % (group, i))
         bump_details.append({
                 'raw_bump': raw_bump,
                 'bump_config': bump_config,

-                'z_channel_config': z_channel_config,

                 'z_axis_config': z_axis_config,
                 'deflection_channel_config': deflection_channel_config,
                 'processed_bump': processed_bump,
                 'z_axis_config': z_axis_config,
                 'deflection_channel_config': deflection_channel_config,
                 'processed_bump': processed_bump,

diff --git a/calibcant/bump.py b/calibcant/bump.py
index 1e2a5b0f97009d3e001b72d2ccacffff1aa27961..90a4b9250459aba8f53d3a89c6c80a3a2ad2bb20 100644 (file)
--- a/calibcant/bump.py
+++ b/calibcant/bump.py
@@ -87,6 +87,7 @@ def bump_acquire(afm, bump_config):
     """
     afm.move_just_onto_surface(
         depth=bump_config['initial-position'], far=bump_config['far-steps'])
     """
     afm.move_just_onto_surface(
         depth=bump_config['initial-position'], far=bump_config['far-steps'])

+    #afm.piezo.jump('z', 32000)

 
     _LOG.info('bump the surface to a depth of %g m'
               % bump_config['push-depth'])
 
     _LOG.info('bump the surface to a depth of %g m'
               % bump_config['push-depth'])


@@ -94,11 +95,9 @@ def bump_acquire(afm, bump_config):
     axis = afm.piezo.axis_by_name(afm.axis_name)
 
     start_pos = afm.piezo.last_output[afm.axis_name]
     axis = afm.piezo.axis_by_name(afm.axis_name)
 
     start_pos = afm.piezo.last_output[afm.axis_name]

-    start_pos_m = _convert_bits_to_meters(
-        axis.axis_channel_config, axis.axis_config, start_pos)
+    start_pos_m = _convert_bits_to_meters(axis.config, start_pos)

     close_pos_m = start_pos_m + bump_config['push-depth']
     close_pos_m = start_pos_m + bump_config['push-depth']

-    close_pos = _convert_meters_to_bits(
-        axis.axis_channel_config, axis.axis_config, close_pos_m)
+    close_pos = _convert_meters_to_bits(axis.config, close_pos_m)

 
     dtype = afm.piezo.channel_dtype(afm.axis_name, direction='output')
     appr = _numpy.linspace(
 
     dtype = afm.piezo.channel_dtype(afm.axis_name, direction='output')
     appr = _numpy.linspace(


@@ -123,7 +122,7 @@ def bump(afm, bump_config, filename, group='/'):
 
     >>> import os
     >>> import tempfile
 
     >>> import os
     >>> import tempfile

-    >>> from h5config.storage.hdf5 import HDF5_Storage, pprint_HDF5
+    >>> from h5config.storage.hdf5 import pprint_HDF5

     >>> from pycomedi.device import Device
     >>> from pycomedi.subdevice import StreamingSubdevice
     >>> from pycomedi.channel import AnalogChannel, DigitalChannel
     >>> from pycomedi.device import Device
     >>> from pycomedi.subdevice import StreamingSubdevice
     >>> from pycomedi.channel import AnalogChannel, DigitalChannel


@@ -132,7 +131,7 @@ def bump(afm, bump_config, filename, group='/'):
     >>> from pypiezo.base import PiezoAxis, InputChannel
     >>> from pypiezo.config import ChannelConfig, AxisConfig
     >>> from stepper import Stepper
     >>> from pypiezo.base import PiezoAxis, InputChannel
     >>> from pypiezo.config import ChannelConfig, AxisConfig
     >>> from stepper import Stepper

-    >>> from pyafm import AFM
+    >>> from pyafm.afm import AFM

     >>> from .config import BumpConfig
 
     >>> fd,filename = tempfile.mkstemp(suffix='.h5', prefix='calibcant-')
     >>> from .config import BumpConfig
 
     >>> fd,filename = tempfile.mkstemp(suffix='.h5', prefix='calibcant-')


@@ -161,26 +160,22 @@ def bump(afm, bump_config, filename, group='/'):
     first few surface approaching steps, which could lead to an
     `EdgeKink` error instead of a `FlatFit` error.
 
     first few surface approaching steps, which could lead to an
     `EdgeKink` error instead of a `FlatFit` error.
 

-    >>> axis_config = AxisConfig(storage=HDF5_Storage(
-    ...         filename=filename, group='/bump/config/z/axis'))
+    >>> axis_config = AxisConfig()

     >>> axis_config.update(
     ...     {'gain':20, 'sensitivity':8e-9, 'minimum':-9})
     >>> axis_config.update(
     ...     {'gain':20, 'sensitivity':8e-9, 'minimum':-9})

-    >>> axis_channel_config = ChannelConfig(storage=HDF5_Storage(
-    ...         filename=filename, group='/bump/config/z/channel'))
-    >>> input_channel_config = ChannelConfig(storage=HDF5_Storage(
-    ...         filename=filename, group='/bump/config/deflection/channel'))
-
-    >>> a = PiezoAxis(axis_config=axis_config,
-    ...     axis_channel_config=axis_channel_config,
-    ...     axis_channel=axis_channel, name='z')
+    >>> axis_channel_config = ChannelConfig()
+    >>> axis_channel_config['name'] = 'z'
+    >>> axis_config['channel'] = axis_channel_config
+    >>> input_channel_config = ChannelConfig()
+    >>> input_channel_config['name'] = 'deflection'
+
+    >>> a = PiezoAxis(config=axis_config, axis_channel=axis_channel)

     >>> a.setup_config()
 
     >>> a.setup_config()
 

-    >>> c = InputChannel(
-    ...     channel_config=input_channel_config, channel=input_channel,
-    ...     name='deflection')
+    >>> c = InputChannel(config=input_channel_config, channel=input_channel)

     >>> c.setup_config()
 
     >>> c.setup_config()
 

-    >>> piezo = AFMPiezo(axes=[a], input_channels=[c])
+    >>> piezo = AFMPiezo(axes=[a], inputs=[c])

 
     Setup a `stepper` instance.
 
 
     Setup a `stepper` instance.
 


@@ -201,11 +196,90 @@ def bump(afm, bump_config, filename, group='/'):
 
     Test a bump:
 
 
     Test a bump:
 

-    >>> bump_config = BumpConfig(storage=HDF5_Storage(
-    ...         filename=filename, group='/bump/config/bump'))
+    >>> bump_config = BumpConfig()

     >>> bump(afm, bump_config, filename, group='/bump')
     TODO: replace skipped example data with real-world values
     >>> pprint_HDF5(filename)  # doctest: +ELLIPSIS, +REPORT_UDIFF
     >>> bump(afm, bump_config, filename, group='/bump')
     TODO: replace skipped example data with real-world values
     >>> pprint_HDF5(filename)  # doctest: +ELLIPSIS, +REPORT_UDIFF

+    /
+      /bump
+        /bump/config
+          /bump/config/bump
+            <HDF5 dataset "far-steps": shape (), type "<i4">
+              200
+            <HDF5 dataset "initial-position": shape (), type "<f8">
+              -5e-08
+            <HDF5 dataset "model": shape (), type "|S9">
+              quadratic
+            <HDF5 dataset "push-depth": shape (), type "<f8">
+              2e-07
+            <HDF5 dataset "push-speed": shape (), type "<f8">
+              1e-06
+            <HDF5 dataset "samples": shape (), type "<i4">
+              1024
+            <HDF5 dataset "setpoint": shape (), type "<f8">
+              2.0
+          /bump/config/deflection
+            /bump/config/deflection/channel
+              <HDF5 dataset "channel": shape (), type "<i4">
+                0
+              <HDF5 dataset "conversion-coefficients": shape (2,), type "<f8">
+                [ -1.00000000e+01   3.05180438e-04]
+              <HDF5 dataset "conversion-origin": shape (), type "<f8">
+                0.0
+              <HDF5 dataset "device": shape (), type "|S12">
+                /dev/comedi0
+              <HDF5 dataset "inverse-conversion-coefficients": shape (2,), type "<f8">
+                [    0.    3276.75]
+              <HDF5 dataset "inverse-conversion-origin": shape (), type "<f8">
+                -10.0
+              <HDF5 dataset "maxdata": shape (), type "<i8">
+                65535
+              <HDF5 dataset "name": shape (), type "|S10">
+                deflection
+              <HDF5 dataset "range": shape (), type "<i4">
+                0
+              <HDF5 dataset "subdevice": shape (), type "<i4">
+                0
+          /bump/config/z
+            /bump/config/z/axis
+              /bump/config/z/axis/channel
+                <HDF5 dataset "channel": shape (), type "<i4">
+                  0
+                <HDF5 dataset "conversion-coefficients": shape (2,), type "<f8">
+                  [ -1.00000000e+01   3.05180438e-04]
+                <HDF5 dataset "conversion-origin": shape (), type "<f8">
+                  0.0
+                <HDF5 dataset "device": shape (), type "|S12">
+                  /dev/comedi0
+                <HDF5 dataset "inverse-conversion-coefficients": shape (2,), type "<f8">
+                  [    0.    3276.75]
+                <HDF5 dataset "inverse-conversion-origin": shape (), type "<f8">
+                  -10.0
+                <HDF5 dataset "maxdata": shape (), type "<i8">
+                  65535
+                <HDF5 dataset "name": shape (), type "|S1">
+                  z
+                <HDF5 dataset "range": shape (), type "<i4">
+                  0
+                <HDF5 dataset "subdevice": shape (), type "<i4">
+                  1
+              <HDF5 dataset "gain": shape (), type "<i4">
+                20
+              <HDF5 dataset "maximum": shape (), type "<f8">
+                10.0
+              <HDF5 dataset "minimum": shape (), type "<i4">
+                -9
+              <HDF5 dataset "monitor": shape (), type "|S1">
+    <BLANKLINE>
+              <HDF5 dataset "sensitivity": shape (), type "<f8">
+                8e-09
+        <HDF5 dataset "processed": shape (), type "<f8">
+          ...
+        /bump/raw
+          <HDF5 dataset "deflection": shape (2048,), type "<u2">
+            [...]
+          <HDF5 dataset "z": shape (2048,), type "<u2">
+            [...]

 
     Close the Comedi device.
 
 
     Close the Comedi device.
 


@@ -220,13 +294,11 @@ def bump(afm, bump_config, filename, group='/'):
 
     data = bump_acquire(afm, bump_config)
     photo_sensitivity = _bump_analyze(
 
     data = bump_acquire(afm, bump_config)
     photo_sensitivity = _bump_analyze(

-        data, bump_config, z_channel_config=axis.axis_channel_config,
-        z_axis_config=axis.axis_config,
-        deflection_channel_config=deflection_channel.channel_config)
+        data, bump_config, z_axis_config=axis.config,
+        deflection_channel_config=deflection_channel.config)

     _bump_save(
         filename, group, data, bump_config,
     _bump_save(
         filename, group, data, bump_config,

-        z_channel_config=axis.axis_channel_config,
-        z_axis_config=axis.axis_config,
-        deflection_channel_config=deflection_channel.channel_config,
+        z_axis_config=axis.config,
+        deflection_channel_config=deflection_channel.config,

         processed_bump=photo_sensitivity)
     return photo_sensitivity
         processed_bump=photo_sensitivity)
     return photo_sensitivity

diff --git a/calibcant/bump_analyze.py b/calibcant/bump_analyze.py
index ab745b812db66439353bada260fd8744e72d0bb6..9f5412e7ae54b1f64d941142844b617127149ef3 100644 (file)
--- a/calibcant/bump_analyze.py
+++ b/calibcant/bump_analyze.py
@@ -87,6 +87,8 @@ measured slope `Vphoto/Vout` is converted to `photo_sensitivity` with
       /bump/config/bump
         <HDF5 dataset "far-steps": shape (), type "<i4">
           200
       /bump/config/bump
         <HDF5 dataset "far-steps": shape (), type "<i4">
           200

+        <HDF5 dataset "initial-position": shape (), type "<f8">
+          -5e-08

         <HDF5 dataset "model": shape (), type "|S9">
           quadratic
         <HDF5 dataset "push-depth": shape (), type "<f8">
         <HDF5 dataset "model": shape (), type "|S9">
           quadratic
         <HDF5 dataset "push-depth": shape (), type "<f8">


@@ -278,6 +280,9 @@ def limited_linear_param_guess(x, y):
     i_high = i
     x_contact = float(x[i_low])
     x_high = float(x[i_high])
     i_high = i
     x_contact = float(x[i_low])
     x_high = float(x[i_high])

+    if x_high == x_contact:
+        x.tofile('x-bad.dat', sep='\n')
+        y.tofile('y-bad.dat', sep='\n')

     slope = (y_high - y_contact) / (x_high - x_contact)
     return (x_contact, y_contact, slope)
 
     slope = (y_high - y_contact) / (x_high - x_contact)
     return (x_contact, y_contact, slope)
 


@@ -368,7 +373,7 @@ def bump_fit(z, deflection, high_voltage_rail,
         _LOG.debug('solution converged')
     else:
         _LOG.debug('solution did not converge')
         _LOG.debug('solution converged')
     else:
         _LOG.debug('solution did not converge')

-    if plot or _package_config['matplotlib'] or True:
+    if plot or _package_config['matplotlib']:

         yguess = model(z, param_guess, high_voltage_rail=high_voltage_rail)
         yfit = model(z, p, high_voltage_rail=high_voltage_rail)
         bump_plot({'z': z, 'deflection': deflection}, yguess=yguess, yfit=yfit)
         yguess = model(z, param_guess, high_voltage_rail=high_voltage_rail)
         yfit = model(z, p, high_voltage_rail=high_voltage_rail)
         bump_plot({'z': z, 'deflection': deflection}, yguess=yguess, yfit=yfit)


@@ -422,7 +427,7 @@ def bump_load(filename, group='/'):
                     filename=filename, group=group+key))
             configs.append(config)
         try:
                     filename=filename, group=group+key))
             configs.append(config)
         try:

-            processed_bump = f[group+'processed'][...]
+            processed_bump = float(f[group+'processed'][...])

         except KeyError:
             pass
     ret = [raw_bump]
         except KeyError:
             pass
     ret = [raw_bump]

diff --git a/calibcant/calibrate.py b/calibcant/calibrate.py
index 426abbf5b686f07143a80b54d2a153eea38cba51..2f850e144742bff1e71b7ad0f5f0fb5fced949f5 100644 (file)
--- a/calibcant/calibrate.py
+++ b/calibcant/calibrate.py
@@ -187,7 +187,7 @@ def calib(afm, calibration_config, filename=None, group='/'):
     >>> from pypiezo.base import PiezoAxis, InputChannel
     >>> from pypiezo.config import ChannelConfig, AxisConfig
     >>> from stepper import Stepper
     >>> from pypiezo.base import PiezoAxis, InputChannel
     >>> from pypiezo.config import ChannelConfig, AxisConfig
     >>> from stepper import Stepper

-    >>> from pyafm import AFM
+    >>> from pyafm.afm import AFM

     >>> from .config import (CalibrationConfig, BumpConfig,
     ...     TemperatureConfig, VibrationConfig)
     >>> from .analyze import calib_load_all
     >>> from .config import (CalibrationConfig, BumpConfig,
     ...     TemperatureConfig, VibrationConfig)
     >>> from .analyze import calib_load_all


@@ -222,19 +222,18 @@ def calib(afm, calibration_config, filename=None, group='/'):
     >>> axis_config.update(
     ...     {'gain':20, 'sensitivity':8e-9, 'minimum':-9})
     >>> axis_channel_config = ChannelConfig()
     >>> axis_config.update(
     ...     {'gain':20, 'sensitivity':8e-9, 'minimum':-9})
     >>> axis_channel_config = ChannelConfig()

+    >>> axis_channel_config['name'] = 'z'
+    >>> axis_config['channel'] = axis_channel_config

     >>> input_channel_config = ChannelConfig()
     >>> input_channel_config = ChannelConfig()

+    >>> input_channel_config['name'] = 'deflection'

 
 

-    >>> a = PiezoAxis(axis_config=axis_config,
-    ...     axis_channel_config=axis_channel_config,
-    ...     axis_channel=axis_channel, name='z')
+    >>> a = PiezoAxis(config=axis_config, axis_channel=axis_channel)

     >>> a.setup_config()
 
     >>> a.setup_config()
 

-    >>> c = InputChannel(
-    ...     channel_config=input_channel_config, channel=input_channel,
-    ...     name='deflection')
+    >>> c = InputChannel(config=input_channel_config, channel=input_channel)

     >>> c.setup_config()
 
     >>> c.setup_config()
 

-    >>> piezo = AFMPiezo(axes=[a], input_channels=[c])
+    >>> piezo = AFMPiezo(axes=[a], inputs=[c])

 
     Setup a `stepper` instance.
 
 
     Setup a `stepper` instance.
 


@@ -256,16 +255,137 @@ def calib(afm, calibration_config, filename=None, group='/'):
     Test calibration:
 
     >>> calibration_config = CalibrationConfig()
     Test calibration:
 
     >>> calibration_config = CalibrationConfig()

-    >>> bump_config = BumpConfig()
-    >>> temperature_config = TemperatureConfig()
-    >>> vibration_config = VibrationConfig()
-    >>> calib(afm, calibration_config, bump_config, temperature_config,
-    ...     vibration_config, filename=filename, group='/')
+    >>> calibration_config['bump'] = BumpConfig()
+    >>> calibration_config['temperature'] = TemperatureConfig()
+    >>> calibration_config['vibration'] = VibrationConfig()
+    >>> calib(afm, calibration_config, filename=filename, group='/')

     TODO: replace skipped example data with real-world values
     >>> pprint_HDF5(filename)  # doctest: +ELLIPSIS, +REPORT_UDIFF
     TODO: replace skipped example data with real-world values
     >>> pprint_HDF5(filename)  # doctest: +ELLIPSIS, +REPORT_UDIFF

+    /
+      /bump
+        /bump/0
+          /bump/0/config
+            /bump/0/config/bump
+              <HDF5 dataset "far-steps": shape (), type "<i4">
+                200
+              ...
+            /bump/0/config/deflection
+              /bump/0/config/deflection/channel
+                <HDF5 dataset "channel": shape (), type "<i4">
+                  0
+                ...
+            /bump/0/config/z
+              /bump/0/config/z/axis
+                /bump/0/config/z/axis/channel
+                  <HDF5 dataset "channel": shape (), type "<i4">
+                    0
+                  ...
+                <HDF5 dataset "gain": shape (), type "<i4">
+                  20
+                ...
+          <HDF5 dataset "processed": shape (), type "<f8">
+            ...
+          /bump/0/raw
+            <HDF5 dataset "deflection": shape (2048,), type "<u2">
+              [...]
+            <HDF5 dataset "z": shape (2048,), type "<u2">
+              [...]
+        /bump/1
+        ...
+      /calibration
+        /calibration/config
+          /calibration/config/bump
+            <HDF5 dataset "far-steps": shape (), type "<i4">
+              200
+            ...
+          <HDF5 dataset "num-bumps": shape (), type "<i4">
+            10
+          ...
+        /calibration/processed
+          /calibration/processed/spring-constant
+            <HDF5 dataset "data": shape (), type "<f8">
+              ...
+            <HDF5 dataset "standard-deviation": shape (), type "<f8">
+              ...
+            <HDF5 dataset "units": shape (), type "|S3">
+              N/m
+        /calibration/raw
+          /calibration/raw/photodiode-sensitivity
+            <HDF5 dataset "data": shape (10,), type "<f8">
+              [...]
+            <HDF5 dataset "units": shape (), type "|S3">
+              V/m
+          /calibration/raw/temperature
+            <HDF5 dataset "data": shape (10,), type "<f8">
+              [...]
+            <HDF5 dataset "units": shape (), type "|S1">
+              K
+          /calibration/raw/thermal-vibration-variance
+            <HDF5 dataset "data": shape (20,), type "<f8">
+              [...]
+            <HDF5 dataset "units": shape (), type "|S3">
+              V^2
+      /temperature
+        /temperature/0
+          /temperature/0/config
+            <HDF5 dataset "default": shape (), type "|b1">
+              False
+            <HDF5 dataset "units": shape (), type "|S7">
+              Celsius
+          <HDF5 dataset "processed": shape (), type "<f8">
+            295.15
+          <HDF5 dataset "raw": shape (), type "<i4">
+            22
+        /temperature/1
+        ...
+      /vibration
+        /vibration/0
+          /vibration/0/config
+            /vibration/0/config/deflection
+              <HDF5 dataset "channel": shape (), type "<i4">
+                0
+              ...
+            /vibration/0/config/vibration
+              <HDF5 dataset "chunk-size": shape (), type "<i4">
+                2048
+              ...
+          <HDF5 dataset "processed": shape (), type "<f8">
+            ...
+          /vibration/0/raw
+            <HDF5 dataset "deflection": shape (65536,), type "<u2">
+              [...]
+        /vibration/1
+        ...
+        /vibration/19
+          ...
+          /vibration/19/raw
+            <HDF5 dataset "deflection": shape (65536,), type "<u2">
+              [...]

     >>> everything = calib_load_all(filename, '/')
     >>> everything = calib_load_all(filename, '/')

-    >>> pprint(everything)
-
+    >>> pprint(everything)  # doctest: +ELLIPSIS, +REPORT_UDIFF
+    {'bump_details': [{'bump_config': <BumpConfig ...>,
+                       'deflection_channel_config': <ChannelConfig ...>,
+                       'processed_bump': ...,
+                       'raw_bump': {'deflection': array([...], dtype=uint16),
+                                    'z': array([...], dtype=uint16)},
+                       'z_axis_config': <AxisConfig ...>},
+                      ...],
+     'bumps': array([...]),
+     'calibration_config': <CalibrationConfig ...>,
+     'k': ...,
+     'k_s': ...,
+     'temperature_details': [{'processed_temperature': ...,
+                              'raw_temperature': array(22),
+                              'temperature_config': <TemperatureConfig ...>},
+                             ...],
+     'temperatures': array([...]),
+     'vibration_details': [{'deflection_channel_config': <ChannelConfig ...>,
+                            'processed_vibration': ...,
+                            'raw_vibration': array([...], dtype=uint16),
+                            'vibration_config': <VibrationConfig ...>},
+                           ...],
+     'vibrations': array([...])}
+     

     Close the Comedi device.
 
     >>> d.close()
     Close the Comedi device.
 
     >>> d.close()


@@ -275,8 +395,7 @@ def calib(afm, calibration_config, filename=None, group='/'):
     os.remove(filename)
     """
     bumps, Ts, vibs = calib_acquire(
     os.remove(filename)
     """
     bumps, Ts, vibs = calib_acquire(

-        afm, calibration_config, bump_config, temperature_config,
-        vibration_config, filename=filename, group=group)
+        afm, calibration_config, filename=filename, group=group)

     # TODO: convert vib units?
     k,k_s = _calib_analyze(bumps, Ts, vibs)
     _calib_save(filename, group=group+'calibration/', bumps=bumps,
     # TODO: convert vib units?
     k,k_s = _calib_analyze(bumps, Ts, vibs)
     _calib_save(filename, group=group+'calibration/', bumps=bumps,

diff --git a/calibcant/config.py b/calibcant/config.py
index cffb58f86d369a404d86970ca6e31099ac01889a..c80e791c1cfe3307a66b67a703bbf39ffc9e518e 100644 (file)
--- a/calibcant/config.py
+++ b/calibcant/config.py
@@ -77,6 +77,12 @@ class Quadratic (_BumpModel):
 class BumpConfig (_config.Config):
     "Configure `calibcant` bump operation"
     settings = [
 class BumpConfig (_config.Config):
     "Configure `calibcant` bump operation"
     settings = [

+        _config.FloatSetting(
+            name='initial-position',
+            help=('Position relative to surface for start of bump in meters.  '
+                  'Should be less than zero to ensure non-contact region '
+                  'before you hit the surface.'),
+            default=-50e-9),

         _config.FloatSetting(
             name='setpoint',
             help=('Maximum deflection in volts in case of stepper positioning '
         _config.FloatSetting(
             name='setpoint',
             help=('Maximum deflection in volts in case of stepper positioning '


@@ -110,9 +116,6 @@ class BumpConfig (_config.Config):
                 ]),
         ]
 
                 ]),
         ]
 

-class BumpResult (_config.Config):
-    "The result of a `calibcant` bump operation"
-    

 
 class _VibrationModel (object):
     pass
 
 class _VibrationModel (object):
     pass

diff --git a/calibcant/vib.py b/calibcant/vib.py
index 608b9b0db4d8e307c948fdff90bb941d0f0245a2..0c71f079e7510f7ec19a6a810d575c4ed9a2b2dc 100644 (file)
--- a/calibcant/vib.py
+++ b/calibcant/vib.py
@@ -114,13 +114,12 @@ def vib(piezo, vibration_config, filename, group='/'):
     >>> channel.range = channel.find_range(
     ...     unit=UNIT.volt, min=-10, max=10)
     >>> channel_config = ChannelConfig()
     >>> channel.range = channel.find_range(
     ...     unit=UNIT.volt, min=-10, max=10)
     >>> channel_config = ChannelConfig()

+    >>> channel_config['name'] = 'deflection'

 
 

-    >>> c = InputChannel(
-    ...     channel_config=channel_config, channel=channel,
-    ...     name='deflection')
+    >>> c = InputChannel(config=channel_config, channel=channel)

     >>> c.setup_config()
 
     >>> c.setup_config()
 

-    >>> piezo = AFMPiezo(axes=[], input_channels=[c])
+    >>> piezo = AFMPiezo(axes=[], inputs=[c])

 
     Test a vibration:
 
 
     Test a vibration:
 


@@ -132,39 +131,40 @@ def vib(piezo, vibration_config, filename, group='/'):
       /vibration
         /vibration/config
           /vibration/config/deflection
       /vibration
         /vibration/config
           /vibration/config/deflection

-            /vibration/config/deflection/channel
-              <HDF5 dataset "channel": shape (), type "|S1">
-                0
-              <HDF5 dataset "conversion-coefficients": shape (), type "|S24">
-                -10.0, 0.000305180437934
-              <HDF5 dataset "conversion-origin": shape (), type "|S3">
-                0.0
-              <HDF5 dataset "device": shape (), type "|S12">
-                /dev/comedi0
-              <HDF5 dataset "inverse-conversion-coefficients": shape (), type "|S12">
-                0.0, 3276.75
-              <HDF5 dataset "inverse-conversion-origin": shape (), type "|S5">
-                -10.0
-              <HDF5 dataset "maxdata": shape (), type "|S5">
-                65535
-              <HDF5 dataset "range": shape (), type "|S1">
-                0
-              <HDF5 dataset "subdevice": shape (), type "|S1">
-                0
+            <HDF5 dataset "channel": shape (), type "<i4">
+              0
+            <HDF5 dataset "conversion-coefficients": shape (2,), type "<f8">
+              [ -1.00000000e+01   3.05180438e-04]
+            <HDF5 dataset "conversion-origin": shape (), type "<f8">
+              0.0
+            <HDF5 dataset "device": shape (), type "|S12">
+              /dev/comedi0
+            <HDF5 dataset "inverse-conversion-coefficients": shape (2,), type "<f8">
+              [    0.    3276.75]
+            <HDF5 dataset "inverse-conversion-origin": shape (), type "<f8">
+              -10.0
+            <HDF5 dataset "maxdata": shape (), type "<i8">
+              65535
+            <HDF5 dataset "name": shape (), type "|S10">
+              deflection
+            <HDF5 dataset "range": shape (), type "<i4">
+              0
+            <HDF5 dataset "subdevice": shape (), type "<i4">
+              0

           /vibration/config/vibration
           /vibration/config/vibration

-            <HDF5 dataset "chunk-size": shape (), type "|S4">
+            <HDF5 dataset "chunk-size": shape (), type "<i4">

               2048
               2048

-            <HDF5 dataset "frequency": shape (), type "|S7">
+            <HDF5 dataset "frequency": shape (), type "<f8">

               50000.0
               50000.0

-            <HDF5 dataset "maximum-fit-frequency": shape (), type "|S7">
+            <HDF5 dataset "maximum-fit-frequency": shape (), type "<f8">

               25000.0
               25000.0

-            <HDF5 dataset "minimum-fit-frequency": shape (), type "|S5">
+            <HDF5 dataset "minimum-fit-frequency": shape (), type "<f8">

               500.0
             <HDF5 dataset "model": shape (), type "|S12">
               Breit-Wigner
               500.0
             <HDF5 dataset "model": shape (), type "|S12">
               Breit-Wigner

-            <HDF5 dataset "overlap": shape (), type "|S2">
-              no
-            <HDF5 dataset "sample-time": shape (), type "|S1">
+            <HDF5 dataset "overlap": shape (), type "|b1">
+              False
+            <HDF5 dataset "sample-time": shape (), type "<i4">

               1
             <HDF5 dataset "window": shape (), type "|S4">
               Hann
               1
             <HDF5 dataset "window": shape (), type "|S4">
               Hann


@@ -184,7 +184,7 @@ def vib(piezo, vibration_config, filename, group='/'):
     """
     deflection_input_channel = piezo.input_channel_by_name('deflection')
     
     """
     deflection_input_channel = piezo.input_channel_by_name('deflection')
     

-    deflection_channel_config = deflection_input_channel.channel_config
+    deflection_channel_config = deflection_input_channel.config

 
     deflection = vib_acquire(piezo, vibration_config)
     variance = _vib_analyze(
 
     deflection = vib_acquire(piezo, vibration_config)
     variance = _vib_analyze(

diff --git a/calibcant/vib_analyze.py b/calibcant/vib_analyze.py
index 6b5d682176fdd023be8c1470cbcedafff2d62d00..bf7455839e3226a6187a8da5f948a9461a80184d 100644 (file)
--- a/calibcant/vib_analyze.py
+++ b/calibcant/vib_analyze.py
@@ -489,7 +489,7 @@ def vib_load(filename, group='/'):
                     filename=filename, group=group+key))
             configs.append(config)
         try:
                     filename=filename, group=group+key))
             configs.append(config)
         try:

-            processed_vibration = f[group+'processed'][...]
+            processed_vibration = float(f[group+'processed'][...])

         except KeyError:
             pass
     ret = [raw_vibration]
         except KeyError:
             pass
     ret = [raw_vibration]